From f9872ba9d65025eb9613821db5e9750408862c67 Mon Sep 17 00:00:00 2001 From: Rhiannon Cameron Date: Mon, 16 Nov 2020 08:59:05 -0800 Subject: [PATCH] InputData DH v0.13.7 - Updated COVID-19 inputData files to be compatible with version 0.13.7. - Added example field data for `purpose of sampling details` and `purpose of sequencing details`. --- .../exampleInput/invalidTestData.csv | 14 +++++++------- .../exampleInput/validTestData.csv | 14 +++++++------- .../exampleInput/validTestData.tsv | 14 +++++++------- .../exampleInput/validTestData.xls | Bin 39424 -> 40960 bytes .../exampleInput/validTestData.xlsx | Bin 50697 -> 51842 bytes 5 files changed, 21 insertions(+), 21 deletions(-) diff --git a/template/canada_covid19/exampleInput/invalidTestData.csv b/template/canada_covid19/exampleInput/invalidTestData.csv index 4ff3f0e0..2c7438fe 100644 --- a/template/canada_covid19/exampleInput/invalidTestData.csv +++ b/template/canada_covid19/exampleInput/invalidTestData.csv @@ -1,7 +1,7 @@ -Database Identifiers,,,,,,,,,,Sample collection and processing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Host Information,,,,,,,,,,,,,,,,Host exposure information,,,,,,,,,,,,Sequencing,,,,,,,,,,,Bioinformatics and QC metrics,,,,,,,,,,,,,,,,,,,,,,,,,,Pathogen diagnostic testing,,,,,,Contributor acknowledgement, -specimen collector sample ID,NML submitted specimen primary ID,NML related specimen primary ID,IRIDA sample name,umbrella bioproject accession,bioproject accession,biosample accession,SRA accession,GenBank accession,GISAID accession,sample collected by,sample collector contact email,sample collector contact address,sequence submitted by,sequence submitter contact email,sequence submitter contact address,sample collection date,sample received date,geo_loc_name (country),geo_loc_name (province/territory),geo_loc_name (city),organism,isolate,purpose of sampling,NML submitted specimen type,NML related specimen relationship type,anatomical material,anatomical part,body product,environmental material,environmental site,collection device,collection method,collection protocol,specimen processing,lab host,passage number,passage method,biomaterial extracted,host (common name),host (scientific name),host health state,host health status details,host health outcome,host disease,host age,host age unit,host age bin,host gender,host origin geo_loc name (country),host subject ID,symptom onset date,signs and symptoms,pre-existing conditions and risk factors,complications,location of exposure geo_loc name (country),destination of most recent travel (city),destination of most recent travel (state/province/territory),destination of most recent travel (country),most recent travel departure date,most recent travel return date,travel history,exposure event,direct/indirect exposure,host role,exposure setting,exposure details,purpose of sequencing,library ID,library insert size,library preparation method,MinIon barcode,sequencing instrument,sequencing protocol name,sequencing protocol source,sequencing kit number,amplicon pcr primers filename,sample sequenced date,raw sequence data processing,sequencing depth (average),assembly name,assembly method,assembly coverage breadth,assembly coverage depth,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,fasta filename,fasta filepath,number base pairs,consensus genome length,mean contig length,N50,Ns per 100 kbp,reference genome accession,consensus sequence ID,consensus sequence method,consensus sequence filename,consensus sequence filepath,annotation feature table filename,bioinformatics protocol,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,authors,DataHarmonizer provenance -Timor-Leste-Handrail-860,SR20-12345,SR20-12340,Timor-Leste-Handrail-860,PRJNA623807,PRJNA855357,SAMN18324170,SRR70983673,KM475726,EPI_ISL_436489,Central East LHIN,scottbethany@gmail.com,"1191 Isabella Street, Unit 70, Campbellford, ON K0L 1L0",,authorativefigure@nwtha.ca,"456 Pleasant Pl, Yellowknife, NT X1A 1O9",3/16/2020,2020-05-28,Canada,Nunavut,Iqualuit,RmYN02,Timor-Leste-Handrail-860,Diagnostic testing,Nucleic acid,Previously Submitted,Fluid (pleural),Pleural sac,Not Applicable,Light switch,Animal house,Fine Needle,Needle Biopsy,PantherFusionSARS-CoV-2,Not applicable,293/ACE2 cell line,15,not applicable,mRNA (cDNA),Lion,Panthera leo,Recovered,Missing,Recovered,Missing,between 45-65,,,Female,USA,nSQu_4,2020-06,Ageusia (complete loss of taste); Cough; Headache; Hypotension (low blood pressure),"Age 60, Smoker",Acute respiratory failure; Guillain-Barré syndrome,USA,New York City,State of New York,United States of America,2020-07-14,2020-07-23,"Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck",Missing,Indirect,Patient,Patient Contact,Exposure setting - in the same common room.,Cluster investigation,Timor-Leste-Handrail-860-1,300,Nextera XT,3225848155,DNBSEQ-G50,NGS protocol v. 12,NGS Libraries,NG5T1LK633,Timor-Leste860_2020-02.txt,2020-07-23,Porechop v. 0.2.3,99x,timor-leste-handrail-86039assembly.fasta,Shovil,91%,17x,Timor-Leste860_S1_L001_R1_001.fastq.gz,Timor-Leste860_S1_L001_R2_001.fastq.gz,/Users/Matthew James/Documents/I./stay dark.fastq.gz,/Users/Heather Gonzalez/Downloads/Development$/,Timor-Leste860_2020-02_batch1a.fast5,/Users/Snyder/Downloads/Concern/.fast5,Timor-Leste860_2020-02_batch1a.fasta,/Users/Phillip Barry/Desktop/,185272,2566,21180,601,865.61,MT_419846.1,SARS-CoV-2_MT3989,,SARS-CoV-2_MT3989.fasta,/Users/Jacqueline/Desktop/Work/Seq/Consensus/,Timor-Leste860_2020-02_Annotation-Features.tbl,Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e,nsp12 (RdRp),Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2,13,ORF7b (ns7b),SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0,6,"Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green",DataHarmonizer: v0.13.3 -NewBrunswick-SARSCoV2-416,SR20-54321,SR20-54320,NewBrunswick-Severeacuterespiratoryvirus2-416,PRJNA623807,PRJNA659224,SAMN14900177,SRR24658112,KY590620,EPI_ISL_461776,,fblack@lhin.on.ca,"0000 Bloor Street West, Toronto, Ontario, M6P 1B1",Alberta ProvLab North (APLN),ab3@cdcab.ca,"3 Ave SE, Calgary, AB R2E 6K9",2020-06-03,30-Apr,Canada,BC,Moncton,RaTG13,NewBrunswick-Severeacuterespiratoryvirus2-416,Surveillance testing,Swab,Previously Submitted,Missing,Lungs,Feces,N95 mask,Clinical assessment centre,Fibrobronchoscope Brush,Air filtration,Shanghai Bio-Germ Medical Technology Co Ltd,Specimens pooled,U251 cell line,22,serial passage in heterologous hosts,RNA (ribo-depleted),Batman,Homo chiroptera,Sick,Not Provided,Not Collected,,89,,80 - 89,Non-binary gender,Bosnia and Herzegovina,rblyp6,2020-03-08,Confusion; Cough; Pharyngitis (sore throat),Bone marrow failure; Metastatic disease; Cardiac disease,Kawasaki disease,Japan,Montreal,Quebec,Canada,2020-05-24,05-2020,"Canada, Alberta; Japan, Tokyo",Occupational exposure (retail),Direct,Other,First Nations Reserve,Host role - Other: Gardener,Diagnostic testing,NewBrunswick-Severeacuterespiratoryvirus2-416;3,200,NEBNext Ultra II,5199601997,HiSeq X Ten,Seq System Protocol v. 0.1.4,BFX-UT_ARTIC_Illumina V 10.4,BDI5MLQMCI6,NB_SARSCoV2-416_2020ampli.txt,05-2020,Deepbinner v. 0.2.0,19x,newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta,Canu,20%,15x,NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz,NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz,/Users/Robert/Downloads/unit-/where item.fastq.gz,"/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz",NB_SARSCoV2-416_2020-seq.fast5,/Users/Kim/Google Drive/his/local-method.fast5,NB_SARSCoV2-416_2020-seq.fasta,/Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta,219669,3787,12664,1214,831.4,NC_045512.1,ConsensusSeq_U0K724,Carthagene v. 1.2,ConsensusSeq_U0K724.fasta,/Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta,NB_SARSCoV2-416_2020-seq-AFT.tbl,Assessing sequence quality in galaxytrakr v 1.2,ORF7a,AllTheTestingPCRing-orf7a v. 2,37,Spike (orf2),2019-nCoV ORF2-gene-v.10,36,"Clyde D. Flores, Tami L. Logan, Amelia M. Foster",DataHarmonizer: v0.13.3 -Mali_RmYN02_eaqr,SR20-13579,SR20-13575,Mali_RmYN02_eaqr,PRJNA623807,PRJNA986922,SAMN16696597,SRR81843993,EU222948,EPI_ISL_518162,BC Centre for Disease Control,rSmith@bccdc.ca,"655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada ",New Brunswick - Vitalité Health Network,Heidi-k@brha.ca,"295 Mountain Rd, Moncton, NB E1C 2N2",2020,2020-05-10,Mali,Not Applicable,Sikasso,SARS-CoV-2,,Missing,mRNA (cDNA),distant relative,liquid,Esophagus,Sputum,,,Needle,Lumbar Puncture,QIAstat-Dx Respiratory SARS-CoV-2 v. 1,RNA re-extraction (post RT-PCR),NHBE cells,Missing,"in vivo, TCID",mRNA,Human,Homo sapiens,Recovered,Hospitalized,Recovered,COVID-19,61,,60 - 69,Undeclared,Kingman Reef,GeV:6,2020-01-10,Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose),Anemia,Abnormal blood oxygen level,Canada,Dublin,Dublin Region,Ireland,15-10-2020,2020-10-30,"Canada, New Brunswick",Convention,Direct,admin,playcare,Direct contact with COVID-19 positive visitor at place of wokr.,testing,ABC-6543211,260,NEBNext Ultra I,6476849764,Illumina Genome Analyzer II,Super Duper Prot. v.1.9,ARTIC Network,CO32934396,Mali_RmYN02_eaqr-amplicon.txt,2020-10-30,Guppy v. 0.5.1,116x,mali_rmyn02_eaqr1assembly.fasta,Velvet,83.65%,111x,Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz,Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz,/Users/Lori/Documents/,/Users/Monica Kelley/Google Drive/staff/girl.fastq.gz,Mali_RmYN02_eaqr-batch2b.fast5,/Users/Hurley/Downloads/seq/,Mali_RmYN02_eaqr-batch2b.fasta,/Users/James/Downloads/be/,157621,6672,5799,1887,419.92,MN988668,SARS-CoV-2_GWA665,FALCON v0.1,SARS-CoV-2_GWA665.fasta,/Users/Watts/Documents/DEN/,Mali_RmYN02_eaqr-annotation.tbl,Pacbio long-read sequencing 0.2.6,N (orf9),SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2,28,ORF6 (ns6),Withalwaysnote_V 6,6,Margaret Holder,DataHarmonizer: v0.13.3 -Newfoundland_Bronchoscope_ISkH,SR20-24680,SR20-24670,Newfoundland_Bronchoscope_ISkH,PRJNA623807,PRJNA627210,SAMN17946661,SRR58371041,KR120562,EPI_ISL_493706,Eastern Health,sshaffer@yahoo.com,"Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6",Manitoba Cadham Provincial Laboratory,someone@wrha.ca,"650 Main St, Winnipeg, MB R3B 1E2",2020-03-06,2020-02-19,Canada,Newfoundland,Stephenville,Severe acute respiratory virus 2,Newfoundland_Bronchoscope_ISkH,Not Applicable,RNA,???,Not Applicable,Eye,Tear,Tissue paper,Bathroom,Collection Cup,Micropipette,AirSurfaceEnvironmentalProtocol v123,Notapplicable,Missing,10,ATCC RSV protocol,mRNA (cDNA),Pig,Sus scrofa domesticus,Not Applicable,Not Applicable,Pig,COVID-19,40-50,,40 - 49,Unknown,Canada,007-Gld-6,3/9/2020,Confusion; Irritability; Cough Cough Cough,Hypertension (high blood pressure); Postpartum (≤6 weeks),COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest,Kosovo,Nice,Provence-Alpes-Cote d'Azur Region,France,2020-09-01,2020-09-03,"Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina",Mass,Unknown,First Responder,Household,Exposure setting - visited personal home for work duty.,,Newfoundland_Bronchoscope_IskH_007,187,Collibri PS DNA Library Prep Kit,3821789592,Ion,pro-seq tech protocol v. 8,NGS protocol v.5.0,LS-2CUO1B,Newfoundland_B-IskH_primer_2020-03.txt,2020-09-03,Cutadapt v. 2.10,127x,newfoundland_B-IskH_assembly.fasta,Canu,56.4%,62x,Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz,Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz,/Users/Nathan Lloyd/Documents/,/Users/Ricky/Google Drive/Window/,Newfoundland_batch03_B-IskH_2020-03.fast5,/Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5,Newfoundland_batch03_B-IskH_2020-03.fasta,/Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta,336858,15187,46431,4921,932.78,SRR80285415,Prov_NOJ678,iVar v. 1.0,Prov_NOJ678-consensus.fasta,/Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta,Newfoundland_anno-table_B-IskH_2020-03.tbl,Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n,nsp15,2019-nCoV nsp 15 v.10,31,ORF1ab (rep),SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3,3,"Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio",DataHarmonizer: v0.13.3 -,SR20-11111,SR20-10000,HospitalMissing555,PRJNA623807,PRJNA981556,SAMN12616187,SRR32188961,MT752147,EPI_ISL_587439,Northern Health,lindseypalmer@northernhealth.ca,"299 Victoria St., Prince George, BC V2L 5B8",Public Health Ontario (PHO),rSmith@gmail.com,"661 University Ave, Toronto, ON M5G 1M1",2020-02-18,2020-05-17,Canda,Manitoba,Brandon,COVID19,HospitalMissing555,Flute,RNA,Acute,Not Applicable,Intestine,Missing,Missing,Wet market,Blood Collection Tube,Necropsy,CanadaPubHealthLab-SARS-CoV-2_v2.3,Specimens pooled,EFK3B cell line,4,"in vivo, serial passage",Not Applicable,Pigeon,Columbidae,Healthy,Missing,Healthy,Missing,86,,80 - 89,Trans,Saint Helena,eEn6,2020-02-13,Cognitive impairment; Fever,Lupus; Sickle cell disease,Unknown,The Moon,Johannesberg,Gauteng Province,south afric,2020-08-08,2020-08-31,"Canada, Toronto; USA, New York City",Family Gathering,Indirect,Visitor,Community Service Centre,Attended convention where multiple people where later diagnosed with COVID-19.,Viral passage experiment,HospitalMissing555-22,312,QIAseq FX DNA,8439507566,NextSeq 500,ABI xl2500 protocol v. 0.3.5,ABI xl2500 protocol V13,YRPJ-JV6P-HVHT,HospitalMissing555_pcr20.txt,10-05-2020,BBTools v. 38.82,129x,hospitalmissing55562assembly.fasta,SPades,32%,4x,HospitalMissing555_S1_L012_R1_001.fastq.gz,HospitalMissing555_S1_L012_R2_001.fastq.gz,/Users/Henry Moss/Desktop/./,/Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz,HospitalMissing555_sequences.fast5,/Users/Walter Bond/Work/,HospitalMissing555_sequences.fasta,/Users/Christopher Martinez/Desktop/administration/,77793,14795,45791,4145,652.11,NC_045512.1,ConsensusSeq_EAQ565,CASAVA 1.8.2,ConsensusSeq_EAQ565.fasta,/Users/Dunlap/Downloads/refgenome/,HospitalMissing555_annotations.tbl,Ncov-2019 sequencing protocol for illumina version 3,E (orf4),Severe acute respiratory syndrome coronavirus 2 real-time PCR E gene 2020 v.0.1,4,ORF7a,2019-nCoV orf7a-v. 2,36,"Thiery Couture, Xian Ch'iu, G'Kora Zanis",DataHarmonizer: v0.13.3 +Database Identifiers,,,,,,,,,,Sample collection and processing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Host Information,,,,,,,,,,,,,,,,Host exposure information,,,,,,,,,,,,Sequencing,,,,,,,,,,,,Bioinformatics and QC metrics,,,,,,,,,,,,,,,,,,,,,,,,,,Pathogen diagnostic testing,,,,,,Contributor acknowledgement, +specimen collector sample ID,NML submitted specimen primary ID,NML related specimen primary ID,IRIDA sample name,umbrella bioproject accession,bioproject accession,biosample accession,SRA accession,GenBank accession,GISAID accession,sample collected by,sample collector contact email,sample collector contact address,sequence submitted by,sequence submitter contact email,sequence submitter contact address,sample collection date,sample received date,geo_loc_name (country),geo_loc_name (province/territory),geo_loc_name (city),organism,isolate,purpose of sampling,purpose of sampling details,NML submitted specimen type,NML related specimen relationship type,anatomical material,anatomical part,body product,environmental material,environmental site,collection device,collection method,collection protocol,specimen processing,lab host,passage number,passage method,biomaterial extracted,host (common name),host (scientific name),host health state,host health status details,host health outcome,host disease,host age,host age unit,host age bin,host gender,host origin geo_loc name (country),host subject ID,symptom onset date,signs and symptoms,pre-existing conditions and risk factors,complications,location of exposure geo_loc name (country),destination of most recent travel (city),destination of most recent travel (state/province/territory),destination of most recent travel (country),most recent travel departure date,most recent travel return date,travel history,exposure event,direct/indirect exposure,host role,exposure setting,exposure details,purpose of sequencing,purpose of sequencing details,library ID,library insert size,library preparation method,MinIon barcode,sequencing instrument,sequencing protocol name,sequencing protocol source,sequencing kit number,amplicon pcr primers filename,sample sequenced date,raw sequence data processing,sequencing depth (average),assembly name,assembly method,assembly coverage breadth,assembly coverage depth,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,fasta filename,fasta filepath,number base pairs,consensus genome length,mean contig length,N50,Ns per 100 kbp,reference genome accession,consensus sequence ID,consensus sequence method,consensus sequence filename,consensus sequence filepath,annotation feature table filename,bioinformatics protocol,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,authors,DataHarmonizer provenance +Timor-Leste-Handrail-860,SR20-12345,SR20-12340,Timor-Leste-Handrail-860,PRJNA623807,PRJNA855357,SAMN18324170,SRR70983673,KM475726,EPI_ISL_436489,Central East LHIN,scottbethany@gmail.com,"1191 Isabella Street, Unit 70, Campbellford, ON K0L 1L0",,authorativefigure@nwtha.ca,"456 Pleasant Pl, Yellowknife, NT X1A 1O9",3/16/2020,2020-05-28,Canada,Nunavut,Iqualuit,RmYN02,Timor-Leste-Handrail-860,Diagnostic testing,Diagnose whether causative agent was SARS-CoV-2 or seasonal influenza.,Nucleic acid,Previously Submitted,Fluid (pleural),Pleural sac,Not Applicable,Light switch,Animal house,Fine Needle,Needle Biopsy,PantherFusionSARS-CoV-2,Not applicable,293/ACE2 cell line,15,not applicable,mRNA (cDNA),Lion,Panthera leo,Recovered,Missing,Recovered,Missing,between 45-65,,,Female,USA,nSQu_4,2020-06,Ageusia (complete loss of taste); Cough; Headache; Hypotension (low blood pressure),"Age 60, Smoker",Acute respiratory failure; Guillain-Barré syndrome,USA,New York City,State of New York,United States of America,2020-07-14,2020-07-23,"Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck",Missing,Indirect,Patient,Patient Contact,Exposure setting - in the same common room.,Cluster investigation,,Timor-Leste-Handrail-860-1,300,Nextera XT,3225848155,DNBSEQ-G50,NGS protocol v. 12,NGS Libraries,NG5T1LK633,Timor-Leste860_2020-02.txt,2020-07-23,Porechop v. 0.2.3,99x,timor-leste-handrail-86039assembly.fasta,Shovil,91%,17x,Timor-Leste860_S1_L001_R1_001.fastq.gz,Timor-Leste860_S1_L001_R2_001.fastq.gz,/Users/Matthew James/Documents/I./stay dark.fastq.gz,/Users/Heather Gonzalez/Downloads/Development$/,Timor-Leste860_2020-02_batch1a.fast5,/Users/Snyder/Downloads/Concern/.fast5,Timor-Leste860_2020-02_batch1a.fasta,/Users/Phillip Barry/Desktop/,185272,2566,21180,601,865.61,MT_419846.1,SARS-CoV-2_MT3989,,SARS-CoV-2_MT3989.fasta,/Users/Jacqueline/Desktop/Work/Seq/Consensus/,Timor-Leste860_2020-02_Annotation-Features.tbl,Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e,nsp12 (RdRp),Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2,13,ORF7b (ns7b),SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0,6,"Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green",DataHarmonizer provenance: v0.13.7 +NewBrunswick-SARSCoV2-416,SR20-54321,SR20-54320,NewBrunswick-Severeacuterespiratoryvirus2-416,PRJNA623807,PRJNA659224,SAMN14900177,SRR24658112,KY590620,EPI_ISL_461776,,fblack@lhin.on.ca,"0000 Bloor Street West, Toronto, Ontario, M6P 1B1",Alberta ProvLab North (APLN),ab3@cdcab.ca,"3 Ave SE, Calgary, AB R2E 6K9",2020-06-03,30-Apr,Canada,BC,Moncton,RaTG13,NewBrunswick-Severeacuterespiratoryvirus2-416,Surveillance testing,The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada.,Swab,Previously Submitted,Missing,Lungs,Feces,N95 mask,Clinical assessment centre,Fibrobronchoscope Brush,Air filtration,Shanghai Bio-Germ Medical Technology Co Ltd,Specimens pooled,U251 cell line,22,serial passage in heterologous hosts,RNA (ribo-depleted),Batman,Homo chiroptera,Sick,Not Provided,Not Collected,,89,,80 - 89,Non-binary gender,Bosnia and Herzegovina,rblyp6,2020-03-08,Confusion; Cough; Pharyngitis (sore throat),Bone marrow failure; Metastatic disease; Cardiac disease,Kawasaki disease,Japan,Montreal,Quebec,Canada,2020-05-24,05-2020,"Canada, Alberta; Japan, Tokyo",Occupational exposure (retail),Direct,Other,First Nations Reserve,Host role - Other: Gardener,Diagnostic testing,Clinical diagnostic sequencing of confirmed COVID-19 patient.,NewBrunswick-Severeacuterespiratoryvirus2-416;3,200,NEBNext Ultra II,5199601997,HiSeq X Ten,Seq System Protocol v. 0.1.4,BFX-UT_ARTIC_Illumina V 10.4,BDI5MLQMCI6,NB_SARSCoV2-416_2020ampli.txt,05-2020,Deepbinner v. 0.2.0,19x,newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta,Canu,20%,15x,NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz,NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz,/Users/Robert/Downloads/unit-/where item.fastq.gz,"/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz",NB_SARSCoV2-416_2020-seq.fast5,/Users/Kim/Google Drive/his/local-method.fast5,NB_SARSCoV2-416_2020-seq.fasta,/Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta,219669,3787,12664,1214,831.4,NC_045512.1,ConsensusSeq_U0K724,Carthagene v. 1.2,ConsensusSeq_U0K724.fasta,/Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta,NB_SARSCoV2-416_2020-seq-AFT.tbl,Assessing sequence quality in galaxytrakr v 1.2,ORF7a,AllTheTestingPCRing-orf7a v. 2,37,Spike (orf2),2019-nCoV ORF2-gene-v.10,36,"Clyde D. Flores, Tami L. Logan, Amelia M. Foster",DataHarmonizer provenance: v0.13.7 +Mali_RmYN02_eaqr,SR20-13579,SR20-13575,Mali_RmYN02_eaqr,PRJNA623807,PRJNA986922,SAMN16696597,SRR81843993,EU222948,EPI_ISL_518162,BC Centre for Disease Control,rSmith@bccdc.ca,"655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada ",New Brunswick - Vitalité Health Network,Heidi-k@brha.ca,"295 Mountain Rd, Moncton, NB E1C 2N2",2020,2020-05-10,Mali,Not Applicable,Sikasso,SARS-CoV-2,,Missing,Missing,mRNA (cDNA),distant relative,liquid,Esophagus,Sputum,,,Needle,Lumbar Puncture,QIAstat-Dx Respiratory SARS-CoV-2 v. 1,RNA re-extraction (post RT-PCR),NHBE cells,Missing,"in vivo, TCID",mRNA,Human,Homo sapiens,Recovered,Hospitalized,Recovered,COVID-19,61,,60 - 69,Undeclared,Kingman Reef,GeV:6,2020-01-10,Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose),Anemia,Abnormal blood oxygen level,Canada,Dublin,Dublin Region,Ireland,15-10-2020,2020-10-30,"Canada, New Brunswick",Convention,Direct,admin,playcare,Direct contact with COVID-19 positive visitor at place of wokr.,testing,The sample was sequenced to investigate the differences in lineages circulating in Canada during the spring and fall waves of the pandemic.,ABC-6543211,260,NEBNext Ultra I,6476849764,Illumina Genome Analyzer II,Super Duper Prot. v.1.9,ARTIC Network,CO32934396,Mali_RmYN02_eaqr-amplicon.txt,2020-10-30,Guppy v. 0.5.1,116x,mali_rmyn02_eaqr1assembly.fasta,Velvet,83.65%,111x,Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz,Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz,/Users/Lori/Documents/,/Users/Monica Kelley/Google Drive/staff/girl.fastq.gz,Mali_RmYN02_eaqr-batch2b.fast5,/Users/Hurley/Downloads/seq/,Mali_RmYN02_eaqr-batch2b.fasta,/Users/James/Downloads/be/,157621,6672,5799,1887,419.92,MN988668,SARS-CoV-2_GWA665,FALCON v0.1,SARS-CoV-2_GWA665.fasta,/Users/Watts/Documents/DEN/,Mali_RmYN02_eaqr-annotation.tbl,Pacbio long-read sequencing 0.2.6,N (orf9),SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2,28,ORF6 (ns6),Withalwaysnote_V 6,6,Margaret Holder,DataHarmonizer provenance: v0.13.7 +Newfoundland_Bronchoscope_ISkH,SR20-24680,SR20-24670,Newfoundland_Bronchoscope_ISkH,PRJNA623807,PRJNA627210,SAMN17946661,SRR58371041,KR120562,EPI_ISL_493706,Eastern Health,sshaffer@yahoo.com,"Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6",Manitoba Cadham Provincial Laboratory,someone@wrha.ca,"650 Main St, Winnipeg, MB R3B 1E2",2020-03-06,2020-02-19,Canada,Newfoundland,Stephenville,Severe acute respiratory virus 2,Newfoundland_Bronchoscope_ISkH,Not Provided,Not Provided,RNA,???,Not Applicable,Eye,Tear,Tissue paper,Bathroom,Collection Cup,Micropipette,AirSurfaceEnvironmentalProtocol v123,Notapplicable,Missing,10,ATCC RSV protocol,mRNA (cDNA),Pig,Sus scrofa domesticus,Not Applicable,Not Applicable,Pig,COVID-19,40-50,,40 - 49,Unknown,Canada,007-Gld-6,3/9/2020,Confusion; Irritability; Cough Cough Cough,Hypertension (high blood pressure); Postpartum (≤6 weeks),COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest,Kosovo,Nice,Provence-Alpes-Cote d'Azur Region,France,2020-09-01,2020-09-03,"Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina",Mass,Unknown,First Responder,Household,Exposure setting - visited personal home for work duty.,,Sequence sampled as part of an enhanced COVID-19 surveillance testing initiative that focuses on retirement homes.,Newfoundland_Bronchoscope_IskH_007,187,Collibri PS DNA Library Prep Kit,3821789592,Ion,pro-seq tech protocol v. 8,NGS protocol v.5.0,LS-2CUO1B,Newfoundland_B-IskH_primer_2020-03.txt,2020-09-03,Cutadapt v. 2.10,127x,newfoundland_B-IskH_assembly.fasta,Canu,56.4%,62x,Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz,Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz,/Users/Nathan Lloyd/Documents/,/Users/Ricky/Google Drive/Window/,Newfoundland_batch03_B-IskH_2020-03.fast5,/Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5,Newfoundland_batch03_B-IskH_2020-03.fasta,/Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta,336858,15187,46431,4921,932.78,SRR80285415,Prov_NOJ678,iVar v. 1.0,Prov_NOJ678-consensus.fasta,/Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta,Newfoundland_anno-table_B-IskH_2020-03.tbl,Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n,nsp15,2019-nCoV nsp 15 v.10,31,ORF1ab (rep),SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3,3,"Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio",DataHarmonizer provenance: v0.13.7 +,SR20-11111,SR20-10000,HospitalMissing555,PRJNA623807,PRJNA981556,SAMN12616187,SRR32188961,MT752147,EPI_ISL_587439,Northern Health,lindseypalmer@northernhealth.ca,"299 Victoria St., Prince George, BC V2L 5B8",Public Health Ontario (PHO),rSmith@gmail.com,"661 University Ave, Toronto, ON M5G 1M1",2020-02-18,2020-05-17,Canda,Manitoba,Brandon,COVID19,HospitalMissing555,Flute,Missing,RNA,Acute,Not Applicable,Intestine,Missing,Missing,Wet market,Blood Collection Tube,Necropsy,CanadaPubHealthLab-SARS-CoV-2_v2.3,Specimens pooled,EFK3B cell line,4,"in vivo, serial passage",Not Applicable,Pigeon,Columbidae,Healthy,Missing,Healthy,Missing,86,,80 - 89,Trans,Saint Helena,eEn6,2020-02-13,Cognitive impairment; Fever,Lupus; Sickle cell disease,Unknown,The Moon,Johannesberg,Gauteng Province,south afric,2020-08-08,2020-08-31,"Canada, Toronto; USA, New York City",Family Gathering,Indirect,Visitor,Community Service Centre,Attended convention where multiple people where later diagnosed with COVID-19.,Viral passage experiment,Study selection of drug-resistant viruses.,HospitalMissing555-22,312,QIAseq FX DNA,8439507566,NextSeq 500,ABI xl2500 protocol v. 0.3.5,ABI xl2500 protocol V13,YRPJ-JV6P-HVHT,HospitalMissing555_pcr20.txt,10-05-2020,BBTools v. 38.82,129x,hospitalmissing55562assembly.fasta,SPades,32%,4x,HospitalMissing555_S1_L012_R1_001.fastq.gz,HospitalMissing555_S1_L012_R2_001.fastq.gz,/Users/Henry Moss/Desktop/./,/Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz,HospitalMissing555_sequences.fast5,/Users/Walter Bond/Work/,HospitalMissing555_sequences.fasta,/Users/Christopher Martinez/Desktop/administration/,77793,14795,45791,4145,652.11,NC_045512.1,ConsensusSeq_EAQ565,CASAVA 1.8.2,ConsensusSeq_EAQ565.fasta,/Users/Dunlap/Downloads/refgenome/,HospitalMissing555_annotations.tbl,Ncov-2019 sequencing protocol for illumina version 3,E (orf4),Severe acute respiratory syndrome coronavirus 2 real-time PCR E gene 2020 v.0.1,4,ORF7a,2019-nCoV orf7a-v. 2,36,"Thiery Couture, Xian Ch'iu, G'Kora Zanis",DataHarmonizer provenance: v0.13.7 diff --git a/template/canada_covid19/exampleInput/validTestData.csv b/template/canada_covid19/exampleInput/validTestData.csv index a554ca98..b3529c34 100644 --- a/template/canada_covid19/exampleInput/validTestData.csv +++ b/template/canada_covid19/exampleInput/validTestData.csv @@ -1,7 +1,7 @@ -Database Identifiers,,,,,,,,,,Sample collection and processing,,,,,,,,,,,,,,,,,,,,,,,,,,,,,Host Information,,,,,,,,,,,,,,,,Host exposure information,,,,,,,,,,,,Sequencing,,,,,,,,,,,Bioinformatics and QC metrics,,,,,,,,,,,,,,,,,,,,,,,,,,Pathogen diagnostic testing,,,,,,Contributor acknowledgement, -specimen collector sample ID,NML submitted specimen primary ID,NML related specimen primary ID,IRIDA sample name,umbrella bioproject accession,bioproject accession,biosample accession,SRA accession,GenBank accession,GISAID accession,sample collected by,sample collector contact email,sample collector contact address,sequence submitted by,sequence submitter contact email,sequence submitter contact address,sample collection date,sample received date,geo_loc_name (country),geo_loc_name (province/territory),geo_loc_name (city),organism,isolate,purpose of sampling,NML submitted specimen type,NML related specimen relationship type,anatomical material,anatomical part,body product,environmental material,environmental site,collection device,collection method,collection protocol,specimen processing,lab host,passage number,passage method,biomaterial extracted,host (common name),host (scientific name),host health state,host health status details,host health outcome,host disease,host age,host age unit,host age bin,host gender,host origin geo_loc name (country),host subject ID,symptom onset date,signs and symptoms,pre-existing conditions and risk factors,complications,location of exposure geo_loc name (country),destination of most recent travel (city),destination of most recent travel (state/province/territory),destination of most recent travel (country),most recent travel departure date,most recent travel return date,travel history,exposure event,direct/indirect exposure,host role,exposure setting,exposure details,purpose of sequencing,library ID,library insert size,library preparation method,MinIon barcode,sequencing instrument,sequencing protocol name,sequencing protocol source,sequencing kit number,amplicon pcr primers filename,sample sequenced date,raw sequence data processing,sequencing depth (average),assembly name,assembly method,assembly coverage breadth,assembly coverage depth,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,fasta filename,fasta filepath,number base pairs,consensus genome length,mean contig length,N50,Ns per 100 kbp,reference genome accession,consensus sequence ID,consensus sequence method,consensus sequence filename,consensus sequence filepath,annotation feature table filename,bioinformatics protocol,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,authors,DataHarmonizer provenance -Timor-Leste-Handrail-860,SR20-12345,SR20-12340,Timor-Leste-Handrail-860,PRJNA623807,PRJNA855357,SAMN18324170,SRR70983673,KM475726,EPI_ISL_436489,Central East LHIN,scottbethany@gmail.com,"1191 Isabella Street, Unit 70, Campbellford, ON K0L 1L0",Canadore College,authorativefigure@nwtha.ca,"456 Pleasant Pl, Yellowknife, NT X1A 1O9",2020-05-09,2020-05-28,Canada,Nunavut,Iqualuit,RmYN02,Timor-Leste-Handrail-860,Diagnostic testing,Nucleic acid,Convalescent,Fluid (pleural),Pleural sac,Not Applicable,Light switch,Animal house,Fine Needle,Needle Biopsy,PantherFusionSARS-CoV-2,Not applicable,293/ACE2 cell line,15,not applicable,mRNA (cDNA),Lion,Panthera leo,Recovered,Missing,Missing,Missing,12,month,0 - 9,Female,United States of America,nSQu_4,2020-03-05,Ageusia (complete loss of taste); Cough; Headache; Hypotension (low blood pressure),Age 60+; Metastatic disease; Smoking,Acute respiratory failure; Guillain-Barré syndrome,United States of America,New York City,New York,United States of America,2020-07-14,2020-07-23,"Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck",Missing,Indirect,Patient,Patient Contact,Exposure setting - in the same common room.,Cluster investigation,Timor-Leste-Handrail-860-1,300,Nextera XT,3225848155,DNBSEQ-G50,NGS protocol v. 12,NGS Libraries,NG5T1LK633,Timor-Leste860_2020-02.txt,2020-09-01,Porechop v. 0.2.3,99x,timor-leste-handrail-86039assembly.fasta,Shovil,91%,17x,Timor-Leste860_S1_L001_R1_001.fastq.gz,Timor-Leste860_S1_L001_R2_001.fastq.gz,/Users/Matthew James/Documents/I./stay dark.fastq.gz,/Users/Heather Gonzalez/Downloads/Development$/,Timor-Leste860_2020-02_batch1a.fast5,/Users/Snyder/Downloads/Concern/.fast5,Timor-Leste860_2020-02_batch1a.fasta,/Users/Phillip Barry/Desktop/,185272,2566,21180,601,865.61,MT_419846.1,SARS-CoV-2_MT3989,CASAVA v. 1.8.2,SARS-CoV-2_MT3989.fasta,/Users/Jacqueline/Desktop/Work/Seq/Consensus/,Timor-Leste860_2020-02_Annotation-Features.tbl,Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e,nsp12 (RdRp),Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2,13,ORF7b (ns7b),SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0,6,"Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green",DataHarmonizer: v0.13.3 -NewBrunswick-SARSCoV2-416,SR20-54321,SR20-54320,NewBrunswick-Severeacuterespiratoryvirus2-416,PRJNA623807,PRJNA659224,SAMN14900177,SRR24658112,KY590620,EPI_ISL_461776,Toronto Central LHIN,fblack@lhin.on.ca,"0000 Bloor Street West, Toronto, Ontario, M6P 1B1",Alberta ProvLab North (APLN),ab3@cdcab.ca,"3 Ave SE, Calgary, AB R2E 6K9",2020-06-03,2020-03-11,Canada,New Brunswick,Moncton,RaTG13,NewBrunswick-Severeacuterespiratoryvirus2-416,Surveillance testing,Swab,Convalescent,Missing,Anus,Feces,N95 mask,Clinical assessment centre,Fibrobronchoscope Brush,Air filtration,Shanghai Bio-Germ Medical Technology Co Ltd,Specimens pooled,U251 cell line,22,serial passage in heterologous hosts,RNA (ribo-depleted),Chicken,Gallus gallus,Not Collected,Not Provided,Stable,Missing,89,year,80 - 89,Non-binary gender,Bosnia and Herzegovina,rblyp6,2020-03-08,Confusion; Cough; Pharyngitis (sore throat),Bone marrow failure; Metastatic disease; Cardiac disease,Kawasaki disease,Japan,Montreal,Quebec,Canada,2020-05-24,2020-05-02,"Canada, Alberta; Japan, Tokyo",Community Event,Direct,Other,First Nations Reserve,Host role - Other: Gardener,Diagnostic testing,NewBrunswick-Severeacuterespiratoryvirus2-416;3,200,NEBNext Ultra II,5199601997,HiSeq X Ten,Seq System Protocol v. 0.1.4,BFX-UT_ARTIC_Illumina V 10.4,BDI5MLQMCI6,NB_SARSCoV2-416_2020ampli.txt,2020-10-20,Deepbinner v. 0.2.0,19x,newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta,Canu,20%,15x,NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz,NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz,/Users/Robert/Downloads/unit-/where item.fastq.gz,"/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz",NB_SARSCoV2-416_2020-seq.fast5,/Users/Kim/Google Drive/his/local-method.fast5,NB_SARSCoV2-416_2020-seq.fasta,/Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta,219669,3787,12664,1214,831.4,NC_045512.1,ConsensusSeq_U0K724,Carthagene v. 1.2,ConsensusSeq_U0K724.fasta,/Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta,NB_SARSCoV2-416_2020-seq-AFT.tbl,Assessing sequence quality in galaxytrakr v 1.2,ORF7a,AllTheTestingPCRing-orf7a v. 2,37,Spike (orf2),2019-nCoV ORF2-gene-v.10,36,"Clyde D. Flores, Tami L. Logan, Amelia M. Foster",DataHarmonizer: v0.13.3 -Mali_RmYN02_eaqr,SR20-13579,SR20-13575,Mali_RmYN02_eaqr,PRJNA623807,PRJNA986922,SAMN16696597,SRR81843993,EU222948,EPI_ISL_518162,BC Centre for Disease Control,rSmith@bccdc.ca,"655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada ",New Brunswick - Vitalité Health Network,Heidi-k@brha.ca,"295 Mountain Rd, Moncton, NB E1C 2N2",2020-03-04,2020-05-10,Canada,Alberta,Sikasso,Severe acute respiratory syndrome coronavirus 2,Mali_RmYN02_eaqr,Missing,mRNA (cDNA),Convalescent,Fluid,Esophagus,Sputum,Hospital gown,School,Needle,Lumbar Puncture,QIAstat-Dx Respiratory SARS-CoV-2 v. 1,RNA re-extraction (post RT-PCR),293/ACE2 cell line,8,"in vivo, TCID",RNA (total),Human,Homo sapiens,Recovered,Hospitalized,Deceased,COVID-19,61,year,60 - 69,Undeclared,Kingman Reef,GeV:6,2020-01-10,Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose),Anemia,Abnormal blood oxygen level,Canada,Dublin,Dublin,Ireland,2020-10-15,2020-10-30,"Canada, New Brunswick",Missing,Direct,Administrator,Daycare,Direct contact with COVID-19 positive visitor at place of wokr.,Research,ABC-6543211,260,NEBNext Ultra I,6476849764,Illumina Genome Analyzer II,Super Duper Prot. v.1.9,ARTIC Network,CO32934396,Mali_RmYN02_eaqr-amplicon.txt,2020-08-31,Guppy v. 0.5.1,116x,mali_rmyn02_eaqr1assembly.fasta,Velvet,83.65%,111x,Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz,Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz,/Users/Lori/Documents/,/Users/Monica Kelley/Google Drive/staff/girl.fastq.gz,Mali_RmYN02_eaqr-batch2b.fast5,/Users/Hurley/Downloads/seq/,Mali_RmYN02_eaqr-batch2b.fasta,/Users/James/Downloads/be/,157621,6672,5799,1887,419.92,MN988668,SARS-CoV-2_GWA665,FALCON v0.1,SARS-CoV-2_GWA665.fasta,/Users/Watts/Documents/DEN/,Mali_RmYN02_eaqr-annotation.tbl,Pacbio long-read sequencing 0.2.6,N (orf9),SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2,28,ORF6 (ns6),Withalwaysnote_V 6,6,Margaret Holder,DataHarmonizer: v0.13.3 -Newfoundland_Bronchoscope_ISkH,SR20-24680,SR20-24670,Newfoundland_Bronchoscope_ISkH,PRJNA623807,PRJNA627210,SAMN17946661,SRR58371041,KR120562,EPI_ISL_493706,Eastern Health,sshaffer@yahoo.com,"Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6",Manitoba Cadham Provincial Laboratory,someone@wrha.ca,"650 Main St, Winnipeg, MB R3B 1E2",2020-03-06,2020-02-19,Canada,Newfoundland and Labrador,Stephenville,Severe acute respiratory syndrome coronavirus 2,Newfoundland_Bronchoscope_ISkH,Not Applicable,RNA,Familial,Not Applicable,Eye,Tear,Tissue paper,Bathroom,Collection Cup,Necropsy,AirSurfaceEnvironmentalProtocol v123,Not applicable,Missing,10,ATCC RSV protocol,mRNA (cDNA),Human,Homo sapiens,Not Applicable,Not Applicable,Recovered,COVID-19,84,year,80 - 89,Male,Canada,007-Gld-6,2020-02-22,Confusion; Irritability; Cough,Hypertension (high blood pressure); Postpartum (≤6 weeks),COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest,Kosovo,Nice,Provence-Alpes-Cote d'Azur,France,2020-09-01,2020-09-03,"Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina",Not Applicable,Unknown,First Responder,Household,Exposure setting - visited personal home for work duty.,Surveillance testing,Newfoundland_Bronchoscope_IskH_007,187,Collibri PS DNA Library Prep Kit,3821789592,Ion Torrent S5 XL,pro-seq tech protocol v. 8,NGS protocol v.5.0,LS-2CUO1B,Newfoundland_B-IskH_primer_2020-03.txt,2020-10-15,Cutadapt v. 2.10,127x,newfoundland_B-IskH_assembly.fasta,Canu,56.4%,62x,Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz,Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz,/Users/Nathan Lloyd/Documents/,/Users/Ricky/Google Drive/Window/,Newfoundland_batch03_B-IskH_2020-03.fast5,/Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5,Newfoundland_batch03_B-IskH_2020-03.fasta,/Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta,336858,15187,46431,4921,932.78,SRR80285415,Prov_NOJ678,iVar v. 1.0,Prov_NOJ678-consensus.fasta,/Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta,Newfoundland_anno-table_B-IskH_2020-03.tbl,Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n,nsp15,2019-nCoV nsp 15 v.10,31,ORF1ab (rep),SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3,3,"Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio",DataHarmonizer: v0.13.3 -HospitalMissing555,SR20-11111,SR20-10000,HospitalMissing555,PRJNA623807,PRJNA981556,SAMN12616187,SRR32188961,MT752147,EPI_ISL_587439,Northern Health,lindseypalmer@northernhealth.ca,"299 Victoria St., Prince George, BC V2L 5B8",Public Health Ontario (PHO),rSmith@gmail.com,"661 University Ave, Toronto, ON M5G 1M1",2020-02-18,2020-05-17,Canada,Manitoba,Brandon,RaTG13,HospitalMissing555,Missing,RNA,Acute,Not Applicable,Intestine,Missing,Missing,Wet market,Blood Collection Tube,Necropsy,CanadaPubHealthLab-SARS-CoV-2_v2.3,Specimens pooled,EFK3B cell line,4,"in vivo, serial passage",Not Applicable,Pigeon,Columbidae,Healthy,Missing,Deteriorating,Missing,86,year,80 - 89,Transgender,Saint Helena,eEn6,2020-02-13,Cognitive impairment; Fever,Lupus; Sickle cell disease,,Canada,Johannesberg,Gauteng,South Africa,2020-08-08,2020-08-31,"Canada, Toronto; USA, New York City",Convention,Indirect,Visitor,Community Service Centre,Attended convention where multiple people where later diagnosed with COVID-19.,Viral passage experiment,HospitalMissing555-22,312,QIAseq FX DNA,8439507566,NextSeq 500,ABI xl2500 protocol v. 0.3.5,ABI xl2500 protocol V13,YRPJ-JV6P-HVHT,HospitalMissing555_pcr20.txt,2020-10-18,BBTools v. 38.82,129x,hospitalmissing55562assembly.fasta,SPades,32%,4x,HospitalMissing555_S1_L012_R1_001.fastq.gz,HospitalMissing555_S1_L012_R2_001.fastq.gz,/Users/Henry Moss/Desktop/./,/Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz,HospitalMissing555_sequences.fast5,/Users/Walter Bond/Work/,HospitalMissing555_sequences.fasta,/Users/Christopher Martinez/Desktop/administration/,77793,14795,45791,4145,652.11,NC_045512.1,ConsensusSeq_EAQ565,CASAVA 1.8.2,ConsensusSeq_EAQ565.fasta,/Users/Dunlap/Downloads/refgenome/,HospitalMissing555_annotations.tbl,Ncov-2019 sequencing protocol for illumina version 3,E (orf4),Severe acute respiratory syndrome 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details,purpose of sequencing,purpose of sequencing details,library ID,library insert size,library preparation method,MinIon barcode,sequencing instrument,sequencing protocol name,sequencing protocol source,sequencing kit number,amplicon pcr primers filename,sample sequenced date,raw sequence data processing,sequencing depth (average),assembly name,assembly method,assembly coverage breadth,assembly coverage depth,r1 fastq filename,r2 fastq filename,r1 fastq filepath,r2 fastq filepath,fast5 filename,fast5 filepath,fasta filename,fasta filepath,number base pairs,consensus genome length,mean contig length,N50,Ns per 100 kbp,reference genome accession,consensus sequence ID,consensus sequence method,consensus sequence filename,consensus sequence filepath,annotation feature table filename,bioinformatics protocol,gene name 1,diagnostic pcr protocol 1,diagnostic pcr Ct value 1,gene name 2,diagnostic pcr protocol 2,diagnostic pcr Ct value 2,authors,DataHarmonizer provenance 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syndrome,United States of America,New York City,New York,United States of America,2020-07-14,2020-07-23,"Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck",Missing,Indirect,Patient,Patient Contact,Exposure setting - in the same common room.,Cluster investigation,Highschool SARS-CoV-2 cluster investigation.,Timor-Leste-Handrail-860-1,300,Nextera XT,3225848155,DNBSEQ-G50,NGS protocol v. 12,NGS Libraries,NG5T1LK633,Timor-Leste860_2020-02.txt,2020-09-01,Porechop v. 0.2.3,99x,timor-leste-handrail-86039assembly.fasta,Shovil,91%,17x,Timor-Leste860_S1_L001_R1_001.fastq.gz,Timor-Leste860_S1_L001_R2_001.fastq.gz,/Users/Matthew James/Documents/I./stay dark.fastq.gz,/Users/Heather Gonzalez/Downloads/Development$/,Timor-Leste860_2020-02_batch1a.fast5,/Users/Snyder/Downloads/Concern/.fast5,Timor-Leste860_2020-02_batch1a.fasta,/Users/Phillip Barry/Desktop/,185272,2566,21180,601,865.61,MT_419846.1,SARS-CoV-2_MT3989,CASAVA v. 1.8.2,SARS-CoV-2_MT3989.fasta,/Users/Jacqueline/Desktop/Work/Seq/Consensus/,Timor-Leste860_2020-02_Annotation-Features.tbl,Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e,nsp12 (RdRp),Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2,13,ORF7b (ns7b),SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0,6,"Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green",DataHarmonizer provenance: v0.13.7 +NewBrunswick-SARSCoV2-416,SR20-54321,SR20-54320,NewBrunswick-Severeacuterespiratoryvirus2-416,PRJNA623807,PRJNA659224,SAMN14900177,SRR24658112,KY590620,EPI_ISL_461776,Toronto Central LHIN,fblack@lhin.on.ca,"0000 Bloor Street West, Toronto, Ontario, M6P 1B1",Alberta ProvLab North (APLN),ab3@cdcab.ca,"3 Ave SE, Calgary, AB R2E 6K9",2020-06-03,2020-03-11,Canada,New Brunswick,Moncton,RaTG13,NewBrunswick-Severeacuterespiratoryvirus2-416,Surveillance testing,The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada.,Swab,Convalescent,Missing,Anus,Feces,N95 mask,Clinical assessment centre,Fibrobronchoscope Brush,Air filtration,Shanghai Bio-Germ Medical Technology Co Ltd,Specimens pooled,U251 cell line,22,serial passage in heterologous hosts,RNA (ribo-depleted),Chicken,Gallus gallus,Not Collected,Not Provided,Stable,Missing,89,year,80 - 89,Non-binary gender,Bosnia and Herzegovina,rblyp6,2020-03-08,Confusion; Cough; Pharyngitis (sore throat),Bone marrow failure; Metastatic disease; Cardiac disease,Kawasaki disease,Japan,Montreal,Quebec,Canada,2020-05-24,2020-05-02,"Canada, Alberta; Japan, Tokyo",Community Event,Direct,Other,First Nations Reserve,Host role - Other: Gardener,Diagnostic testing,Clinical diagnostic sequencing of confirmed COVID-19 patient.,NewBrunswick-Severeacuterespiratoryvirus2-416;3,200,NEBNext Ultra II,5199601997,HiSeq X Ten,Seq System Protocol v. 0.1.4,BFX-UT_ARTIC_Illumina V 10.4,BDI5MLQMCI6,NB_SARSCoV2-416_2020ampli.txt,2020-10-20,Deepbinner v. 0.2.0,19x,newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta,Canu,20%,15x,NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz,NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz,/Users/Robert/Downloads/unit-/where item.fastq.gz,"/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz",NB_SARSCoV2-416_2020-seq.fast5,/Users/Kim/Google Drive/his/local-method.fast5,NB_SARSCoV2-416_2020-seq.fasta,/Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta,219669,3787,12664,1214,831.4,NC_045512.1,ConsensusSeq_U0K724,Carthagene v. 1.2,ConsensusSeq_U0K724.fasta,/Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta,NB_SARSCoV2-416_2020-seq-AFT.tbl,Assessing sequence quality in galaxytrakr v 1.2,ORF7a,AllTheTestingPCRing-orf7a v. 2,37,Spike (orf2),2019-nCoV ORF2-gene-v.10,36,"Clyde D. Flores, Tami L. Logan, Amelia M. Foster",DataHarmonizer provenance: v0.13.7 +Mali_RmYN02_eaqr,SR20-13579,SR20-13575,Mali_RmYN02_eaqr,PRJNA623807,PRJNA986922,SAMN16696597,SRR81843993,EU222948,EPI_ISL_518162,BC Centre for Disease Control,rSmith@bccdc.ca,"655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada ",New Brunswick - Vitalité Health Network,Heidi-k@brha.ca,"295 Mountain Rd, Moncton, NB E1C 2N2",2020-03-04,2020-05-10,Canada,Alberta,Sikasso,Severe acute respiratory syndrome coronavirus 2,Mali_RmYN02_eaqr,Missing,Missing,mRNA (cDNA),Convalescent,Fluid,Esophagus,Sputum,Hospital gown,School,Needle,Lumbar Puncture,QIAstat-Dx Respiratory SARS-CoV-2 v. 1,RNA re-extraction (post RT-PCR),293/ACE2 cell line,8,"in vivo, TCID",RNA (total),Human,Homo sapiens,Recovered,Hospitalized,Deceased,COVID-19,61,year,60 - 69,Undeclared,Kingman Reef,GeV:6,2020-01-10,Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose),Anemia,Abnormal blood oxygen level,Canada,Dublin,Dublin,Ireland,2020-10-15,2020-10-30,"Canada, New Brunswick",Missing,Direct,Administrator,Daycare,Direct contact with COVID-19 positive visitor at place of wokr.,Research,The sample was sequenced to investigate the differences in lineages circulating in Canada during the spring and fall waves of the pandemic.,ABC-6543211,260,NEBNext Ultra I,6476849764,Illumina Genome Analyzer II,Super Duper Prot. v.1.9,ARTIC Network,CO32934396,Mali_RmYN02_eaqr-amplicon.txt,2020-08-31,Guppy v. 0.5.1,116x,mali_rmyn02_eaqr1assembly.fasta,Velvet,83.65%,111x,Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz,Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz,/Users/Lori/Documents/,/Users/Monica Kelley/Google Drive/staff/girl.fastq.gz,Mali_RmYN02_eaqr-batch2b.fast5,/Users/Hurley/Downloads/seq/,Mali_RmYN02_eaqr-batch2b.fasta,/Users/James/Downloads/be/,157621,6672,5799,1887,419.92,MN988668,SARS-CoV-2_GWA665,FALCON v0.1,SARS-CoV-2_GWA665.fasta,/Users/Watts/Documents/DEN/,Mali_RmYN02_eaqr-annotation.tbl,Pacbio long-read sequencing 0.2.6,N (orf9),SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2,28,ORF6 (ns6),Withalwaysnote_V 6,6,Margaret Holder,DataHarmonizer provenance: v0.13.7 +Newfoundland_Bronchoscope_ISkH,SR20-24680,SR20-24670,Newfoundland_Bronchoscope_ISkH,PRJNA623807,PRJNA627210,SAMN17946661,SRR58371041,KR120562,EPI_ISL_493706,Eastern Health,sshaffer@yahoo.com,"Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6",Manitoba Cadham Provincial Laboratory,someone@wrha.ca,"650 Main St, Winnipeg, MB R3B 1E2",2020-03-06,2020-02-19,Canada,Newfoundland and Labrador,Stephenville,Severe acute respiratory syndrome coronavirus 2,Newfoundland_Bronchoscope_ISkH,Not Provided,Not Provided,RNA,Familial,Not Applicable,Eye,Tear,Tissue paper,Bathroom,Collection Cup,Necropsy,AirSurfaceEnvironmentalProtocol v123,Not applicable,Missing,10,ATCC RSV protocol,mRNA (cDNA),Human,Homo sapiens,Not Applicable,Not Applicable,Recovered,COVID-19,84,year,80 - 89,Male,Canada,007-Gld-6,2020-02-22,Confusion; Irritability; Cough,Hypertension (high blood pressure); Postpartum (≤6 weeks),COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest,Kosovo,Nice,Provence-Alpes-Cote d'Azur,France,2020-09-01,2020-09-03,"Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina",Not Applicable,Unknown,First Responder,Household,Exposure setting - visited personal home for work duty.,Surveillance testing,Sequence sampled as part of an enhanced COVID-19 surveillance testing initiative that focuses on retirement homes.,Newfoundland_Bronchoscope_IskH_007,187,Collibri PS DNA Library Prep Kit,3821789592,Ion Torrent S5 XL,pro-seq tech protocol v. 8,NGS protocol v.5.0,LS-2CUO1B,Newfoundland_B-IskH_primer_2020-03.txt,2020-10-15,Cutadapt v. 2.10,127x,newfoundland_B-IskH_assembly.fasta,Canu,56.4%,62x,Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz,Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz,/Users/Nathan Lloyd/Documents/,/Users/Ricky/Google Drive/Window/,Newfoundland_batch03_B-IskH_2020-03.fast5,/Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5,Newfoundland_batch03_B-IskH_2020-03.fasta,/Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta,336858,15187,46431,4921,932.78,SRR80285415,Prov_NOJ678,iVar v. 1.0,Prov_NOJ678-consensus.fasta,/Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta,Newfoundland_anno-table_B-IskH_2020-03.tbl,Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n,nsp15,2019-nCoV nsp 15 v.10,31,ORF1ab (rep),SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3,3,"Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio",DataHarmonizer provenance: v0.13.7 +HospitalMissing555,SR20-11111,SR20-10000,HospitalMissing555,PRJNA623807,PRJNA981556,SAMN12616187,SRR32188961,MT752147,EPI_ISL_587439,Northern Health,lindseypalmer@northernhealth.ca,"299 Victoria St., Prince George, BC V2L 5B8",Public Health Ontario (PHO),rSmith@gmail.com,"661 University Ave, Toronto, ON M5G 1M1",2020-02-18,2020-05-17,Canada,Manitoba,Brandon,RaTG13,HospitalMissing555,Missing,Missing,RNA,Acute,Not Applicable,Intestine,Missing,Missing,Wet market,Blood Collection Tube,Necropsy,CanadaPubHealthLab-SARS-CoV-2_v2.3,Specimens pooled,EFK3B cell line,4,"in vivo, serial passage",Not Applicable,Pigeon,Columbidae,Healthy,Missing,Deteriorating,Missing,86,year,80 - 89,Transgender,Saint Helena,eEn6,2020-02-13,Cognitive impairment; Fever,Lupus; Sickle cell disease,,Canada,Johannesberg,Gauteng,South Africa,2020-08-08,2020-08-31,"Canada, Toronto; USA, New York City",Convention,Indirect,Visitor,Community Service Centre,Attended convention where multiple people where later diagnosed with COVID-19.,Viral passage experiment,Study selection of drug-resistant viruses.,HospitalMissing555-22,312,QIAseq FX DNA,8439507566,NextSeq 500,ABI xl2500 protocol v. 0.3.5,ABI xl2500 protocol V13,YRPJ-JV6P-HVHT,HospitalMissing555_pcr20.txt,2020-10-18,BBTools v. 38.82,129x,hospitalmissing55562assembly.fasta,SPades,32%,4x,HospitalMissing555_S1_L012_R1_001.fastq.gz,HospitalMissing555_S1_L012_R2_001.fastq.gz,/Users/Henry Moss/Desktop/./,/Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz,HospitalMissing555_sequences.fast5,/Users/Walter Bond/Work/,HospitalMissing555_sequences.fasta,/Users/Christopher Martinez/Desktop/administration/,77793,14795,45791,4145,652.11,NC_045512.1,ConsensusSeq_EAQ565,CASAVA 1.8.2,ConsensusSeq_EAQ565.fasta,/Users/Dunlap/Downloads/refgenome/,HospitalMissing555_annotations.tbl,Ncov-2019 sequencing protocol for illumina version 3,E (orf4),Severe acute respiratory syndrome coronavirus 2 real-time PCR E gene 2020 v.0.1,4,ORF7a,2019-nCoV orf7a-v. 2,36,"Thiery Couture, Xian Ch'iu, G'Kora Zanis",DataHarmonizer provenance: v0.13.7 diff --git a/template/canada_covid19/exampleInput/validTestData.tsv b/template/canada_covid19/exampleInput/validTestData.tsv index dd68dcfd..257c497c 100644 --- a/template/canada_covid19/exampleInput/validTestData.tsv +++ b/template/canada_covid19/exampleInput/validTestData.tsv @@ -1,7 +1,7 @@ -Database Identifiers Sample collection and processing Host Information Host exposure information Sequencing Bioinformatics and QC metrics Pathogen diagnostic testing Contributor acknowledgement -specimen collector sample ID NML submitted specimen primary ID NML related specimen primary ID IRIDA sample name umbrella bioproject accession bioproject accession biosample accession SRA accession GenBank accession GISAID accession sample collected by sample collector contact email sample collector contact address sequence submitted by sequence submitter contact email sequence submitter contact address sample collection date sample received date geo_loc_name (country) geo_loc_name (province/territory) geo_loc_name (city) organism isolate purpose of sampling NML submitted specimen type NML related specimen relationship type anatomical material anatomical part body product environmental material environmental site collection device collection method collection protocol specimen processing lab host passage number passage method biomaterial extracted host (common name) host (scientific name) host health state host health status details host health outcome host disease host age host age unit host age bin host gender host origin geo_loc name (country) host subject ID symptom onset date signs and symptoms pre-existing conditions and risk factors complications location of exposure geo_loc name (country) destination of most recent travel (city) destination of most recent travel (state/province/territory) destination of most recent travel (country) most recent travel departure date most recent travel return date travel history exposure event direct/indirect exposure host role exposure setting exposure details purpose of sequencing library ID library insert size library preparation method MinIon barcode sequencing instrument sequencing protocol name sequencing protocol source sequencing kit number amplicon pcr primers filename sample sequenced date raw sequence data processing sequencing depth (average) assembly name assembly method assembly coverage breadth assembly coverage depth r1 fastq filename r2 fastq filename r1 fastq filepath r2 fastq filepath fast5 filename fast5 filepath fasta filename fasta filepath number base pairs consensus genome length mean contig length N50 Ns per 100 kbp reference genome accession consensus sequence ID consensus sequence method consensus sequence filename consensus sequence filepath annotation feature table filename bioinformatics protocol gene name 1 diagnostic pcr protocol 1 diagnostic pcr Ct value 1 gene name 2 diagnostic pcr protocol 2 diagnostic pcr Ct value 2 authors DataHarmonizer provenance -Timor-Leste-Handrail-860 SR20-12345 SR20-12340 Timor-Leste-Handrail-860 PRJNA623807 PRJNA855357 SAMN18324170 SRR70983673 KM475726 EPI_ISL_436489 Central East LHIN scottbethany@gmail.com 1191 Isabella Street, Unit 70, Campbellford, ON K0L 1L0 Canadore College authorativefigure@nwtha.ca 456 Pleasant Pl, Yellowknife, NT X1A 1O9 2020-05-09 2020-05-28 Canada Nunavut Iqualuit RmYN02 Timor-Leste-Handrail-860 Diagnostic testing Nucleic acid Convalescent Fluid (pleural) Pleural sac Not Applicable Light switch Animal house Fine Needle Needle Biopsy PantherFusionSARS-CoV-2 Not applicable 293/ACE2 cell line 15 not applicable mRNA (cDNA) Lion Panthera leo Recovered Missing Missing Missing 12 month 0 - 9 Female United States of America nSQu_4 2020-03-05 Ageusia (complete loss of taste); Cough; Headache; Hypotension (low blood pressure) Age 60+; Metastatic disease; Smoking Acute respiratory failure; Guillain-Barré syndrome United States of America New York City New York United States of America 2020-07-14 2020-07-23 Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck Missing Indirect Patient Patient Contact Exposure setting - in the same common room. Cluster investigation Timor-Leste-Handrail-860-1 300 Nextera XT 3225848155 DNBSEQ-G50 NGS protocol v. 12 NGS Libraries NG5T1LK633 Timor-Leste860_2020-02.txt 2020-09-01 Porechop v. 0.2.3 99x timor-leste-handrail-86039assembly.fasta Shovil 91% 17x Timor-Leste860_S1_L001_R1_001.fastq.gz Timor-Leste860_S1_L001_R2_001.fastq.gz /Users/Matthew James/Documents/I./stay dark.fastq.gz /Users/Heather Gonzalez/Downloads/Development$/ Timor-Leste860_2020-02_batch1a.fast5 /Users/Snyder/Downloads/Concern/.fast5 Timor-Leste860_2020-02_batch1a.fasta /Users/Phillip Barry/Desktop/ 185272 2566 21180 601 865.61 MT_419846.1 SARS-CoV-2_MT3989 CASAVA v. 1.8.2 SARS-CoV-2_MT3989.fasta /Users/Jacqueline/Desktop/Work/Seq/Consensus/ Timor-Leste860_2020-02_Annotation-Features.tbl Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e nsp12 (RdRp) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2 13 ORF7b (ns7b) SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0 6 Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green DataHarmonizer: v0.13.3 -NewBrunswick-SARSCoV2-416 SR20-54321 SR20-54320 NewBrunswick-Severeacuterespiratoryvirus2-416 PRJNA623807 PRJNA659224 SAMN14900177 SRR24658112 KY590620 EPI_ISL_461776 Toronto Central LHIN fblack@lhin.on.ca 0000 Bloor Street West, Toronto, Ontario, M6P 1B1 Alberta ProvLab North (APLN) ab3@cdcab.ca 3 Ave SE, Calgary, AB R2E 6K9 2020-06-03 2020-03-11 Canada New Brunswick Moncton RaTG13 NewBrunswick-Severeacuterespiratoryvirus2-416 Surveillance testing Swab Convalescent Missing Anus Feces N95 mask Clinical assessment centre Fibrobronchoscope Brush Air filtration Shanghai Bio-Germ Medical Technology Co Ltd Specimens pooled U251 cell line 22 serial passage in heterologous hosts RNA (ribo-depleted) Chicken Gallus gallus Not Collected Not Provided Stable Missing 89 year 80 - 89 Non-binary gender Bosnia and Herzegovina rblyp6 2020-03-08 Confusion; Cough; Pharyngitis (sore throat) Bone marrow failure; Metastatic disease; Cardiac disease Kawasaki disease Japan Montreal Quebec Canada 2020-05-24 2020-05-02 Canada, Alberta; Japan, Tokyo Community Event Direct Other First Nations Reserve Host role - Other: Gardener Diagnostic testing NewBrunswick-Severeacuterespiratoryvirus2-416;3 200 NEBNext Ultra II 5199601997 HiSeq X Ten Seq System Protocol v. 0.1.4 BFX-UT_ARTIC_Illumina V 10.4 BDI5MLQMCI6 NB_SARSCoV2-416_2020ampli.txt 2020-10-20 Deepbinner v. 0.2.0 19x newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta Canu 20% 15x NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz /Users/Robert/Downloads/unit-/where item.fastq.gz "/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz" NB_SARSCoV2-416_2020-seq.fast5 /Users/Kim/Google Drive/his/local-method.fast5 NB_SARSCoV2-416_2020-seq.fasta /Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta 219669 3787 12664 1214 831.4 NC_045512.1 ConsensusSeq_U0K724 Carthagene v. 1.2 ConsensusSeq_U0K724.fasta /Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta NB_SARSCoV2-416_2020-seq-AFT.tbl Assessing sequence quality in galaxytrakr v 1.2 ORF7a AllTheTestingPCRing-orf7a v. 2 37 Spike (orf2) 2019-nCoV ORF2-gene-v.10 36 Clyde D. Flores, Tami L. Logan, Amelia M. Foster DataHarmonizer: v0.13.3 -Mali_RmYN02_eaqr SR20-13579 SR20-13575 Mali_RmYN02_eaqr PRJNA623807 PRJNA986922 SAMN16696597 SRR81843993 EU222948 EPI_ISL_518162 BC Centre for Disease Control rSmith@bccdc.ca 655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada New Brunswick - Vitalité Health Network Heidi-k@brha.ca 295 Mountain Rd, Moncton, NB E1C 2N2 2020-03-04 2020-05-10 Canada Alberta Sikasso Severe acute respiratory syndrome coronavirus 2 Mali_RmYN02_eaqr Missing mRNA (cDNA) Convalescent Fluid Esophagus Sputum Hospital gown School Needle Lumbar Puncture QIAstat-Dx Respiratory SARS-CoV-2 v. 1 RNA re-extraction (post RT-PCR) 293/ACE2 cell line 8 in vivo, TCID RNA (total) Human Homo sapiens Recovered Hospitalized Deceased COVID-19 61 year 60 - 69 Undeclared Kingman Reef GeV:6 2020-01-10 Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose) Anemia Abnormal blood oxygen level Canada Dublin Dublin Ireland 2020-10-15 2020-10-30 Canada, New Brunswick Missing Direct Administrator Daycare Direct contact with COVID-19 positive visitor at place of wokr. Research ABC-6543211 260 NEBNext Ultra I 6476849764 Illumina Genome Analyzer II Super Duper Prot. v.1.9 ARTIC Network CO32934396 Mali_RmYN02_eaqr-amplicon.txt 2020-08-31 Guppy v. 0.5.1 116x mali_rmyn02_eaqr1assembly.fasta Velvet 83.65% 111x Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz /Users/Lori/Documents/ /Users/Monica Kelley/Google Drive/staff/girl.fastq.gz Mali_RmYN02_eaqr-batch2b.fast5 /Users/Hurley/Downloads/seq/ Mali_RmYN02_eaqr-batch2b.fasta /Users/James/Downloads/be/ 157621 6672 5799 1887 419.92 MN988668 SARS-CoV-2_GWA665 FALCON v0.1 SARS-CoV-2_GWA665.fasta /Users/Watts/Documents/DEN/ Mali_RmYN02_eaqr-annotation.tbl Pacbio long-read sequencing 0.2.6 N (orf9) SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2 28 ORF6 (ns6) Withalwaysnote_V 6 6 Margaret Holder DataHarmonizer: v0.13.3 -Newfoundland_Bronchoscope_ISkH SR20-24680 SR20-24670 Newfoundland_Bronchoscope_ISkH PRJNA623807 PRJNA627210 SAMN17946661 SRR58371041 KR120562 EPI_ISL_493706 Eastern Health sshaffer@yahoo.com Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6 Manitoba Cadham Provincial Laboratory someone@wrha.ca 650 Main St, Winnipeg, MB R3B 1E2 2020-03-06 2020-02-19 Canada Newfoundland and Labrador Stephenville Severe acute respiratory syndrome coronavirus 2 Newfoundland_Bronchoscope_ISkH Not Applicable RNA Familial Not Applicable Eye Tear Tissue paper Bathroom Collection Cup Necropsy AirSurfaceEnvironmentalProtocol v123 Not applicable Missing 10 ATCC RSV protocol mRNA (cDNA) Human Homo sapiens Not Applicable Not Applicable Recovered COVID-19 84 year 80 - 89 Male Canada 007-Gld-6 2020-02-22 Confusion; Irritability; Cough Hypertension (high blood pressure); Postpartum (≤6 weeks) COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest Kosovo Nice Provence-Alpes-Cote d'Azur France 2020-09-01 2020-09-03 Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina Not Applicable Unknown First Responder Household Exposure setting - visited personal home for work duty. Surveillance testing Newfoundland_Bronchoscope_IskH_007 187 Collibri PS DNA Library Prep Kit 3821789592 Ion Torrent S5 XL pro-seq tech protocol v. 8 NGS protocol v.5.0 LS-2CUO1B Newfoundland_B-IskH_primer_2020-03.txt 2020-10-15 Cutadapt v. 2.10 127x newfoundland_B-IskH_assembly.fasta Canu 56.4% 62x Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz /Users/Nathan Lloyd/Documents/ /Users/Ricky/Google Drive/Window/ Newfoundland_batch03_B-IskH_2020-03.fast5 /Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5 Newfoundland_batch03_B-IskH_2020-03.fasta /Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta 336858 15187 46431 4921 932.78 SRR80285415 Prov_NOJ678 iVar v. 1.0 Prov_NOJ678-consensus.fasta /Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta Newfoundland_anno-table_B-IskH_2020-03.tbl Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n nsp15 2019-nCoV nsp 15 v.10 31 ORF1ab (rep) SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3 3 Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio DataHarmonizer: v0.13.3 -HospitalMissing555 SR20-11111 SR20-10000 HospitalMissing555 PRJNA623807 PRJNA981556 SAMN12616187 SRR32188961 MT752147 EPI_ISL_587439 Northern Health lindseypalmer@northernhealth.ca 299 Victoria St., Prince George, BC V2L 5B8 Public Health Ontario (PHO) rSmith@gmail.com 661 University Ave, Toronto, ON M5G 1M1 2020-02-18 2020-05-17 Canada Manitoba Brandon RaTG13 HospitalMissing555 Missing RNA Acute Not Applicable Intestine Missing Missing Wet market Blood Collection Tube Necropsy CanadaPubHealthLab-SARS-CoV-2_v2.3 Specimens pooled EFK3B cell line 4 in vivo, serial passage Not Applicable Pigeon Columbidae Healthy Missing Deteriorating Missing 86 year 80 - 89 Transgender Saint Helena eEn6 2020-02-13 Cognitive impairment; Fever Lupus; Sickle cell disease Canada Johannesberg Gauteng South Africa 2020-08-08 2020-08-31 Canada, Toronto; USA, New York City Convention Indirect Visitor Community Service Centre Attended convention where multiple people where later diagnosed with COVID-19. Viral passage experiment HospitalMissing555-22 312 QIAseq FX DNA 8439507566 NextSeq 500 ABI xl2500 protocol v. 0.3.5 ABI xl2500 protocol V13 YRPJ-JV6P-HVHT HospitalMissing555_pcr20.txt 2020-10-18 BBTools v. 38.82 129x hospitalmissing55562assembly.fasta SPades 32% 4x HospitalMissing555_S1_L012_R1_001.fastq.gz HospitalMissing555_S1_L012_R2_001.fastq.gz /Users/Henry Moss/Desktop/./ /Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz HospitalMissing555_sequences.fast5 /Users/Walter Bond/Work/ HospitalMissing555_sequences.fasta /Users/Christopher Martinez/Desktop/administration/ 77793 14795 45791 4145 652.11 NC_045512.1 ConsensusSeq_EAQ565 CASAVA 1.8.2 ConsensusSeq_EAQ565.fasta /Users/Dunlap/Downloads/refgenome/ HospitalMissing555_annotations.tbl Ncov-2019 sequencing protocol for illumina version 3 E (orf4) Severe acute respiratory syndrome coronavirus 2 real-time PCR E gene 2020 v.0.1 4 ORF7a 2019-nCoV orf7a-v. 2 36 Thiery Couture, Xian Ch'iu, G'Kora Zanis DataHarmonizer: v0.13.3 +Database Identifiers Sample collection and processing Host Information Host exposure information Sequencing Bioinformatics and QC metrics Pathogen diagnostic testing Contributor acknowledgement +specimen collector sample ID NML submitted specimen primary ID NML related specimen primary ID IRIDA sample name umbrella bioproject accession bioproject accession biosample accession SRA accession GenBank accession GISAID accession sample collected by sample collector contact email sample collector contact address sequence submitted by sequence submitter contact email sequence submitter contact address sample collection date sample received date geo_loc_name (country) geo_loc_name (province/territory) geo_loc_name (city) organism isolate purpose of sampling purpose of sampling details NML submitted specimen type NML related specimen relationship type anatomical material anatomical part body product environmental material environmental site collection device collection method collection protocol specimen processing lab host passage number passage method biomaterial extracted host (common name) host (scientific name) host health state host health status details host health outcome host disease host age host age unit host age bin host gender host origin geo_loc name (country) host subject ID symptom onset date signs and symptoms pre-existing conditions and risk factors complications location of exposure geo_loc name (country) destination of most recent travel (city) destination of most recent travel (state/province/territory) destination of most recent travel (country) most recent travel departure date most recent travel return date travel history exposure event direct/indirect exposure host role exposure setting exposure details purpose of sequencing purpose of sequencing details library ID library insert size library preparation method MinIon barcode sequencing instrument sequencing protocol name sequencing protocol source sequencing kit number amplicon pcr primers filename sample sequenced date raw sequence data processing sequencing depth (average) assembly name assembly method assembly coverage breadth assembly coverage depth r1 fastq filename r2 fastq filename r1 fastq filepath r2 fastq filepath fast5 filename fast5 filepath fasta filename fasta filepath number base pairs consensus genome length mean contig length N50 Ns per 100 kbp reference genome accession consensus sequence ID consensus sequence method consensus sequence filename consensus sequence filepath annotation feature table filename bioinformatics protocol gene name 1 diagnostic pcr protocol 1 diagnostic pcr Ct value 1 gene name 2 diagnostic pcr protocol 2 diagnostic pcr Ct value 2 authors DataHarmonizer provenance +Timor-Leste-Handrail-860 SR20-12345 SR20-12340 Timor-Leste-Handrail-860 PRJNA623807 PRJNA855357 SAMN18324170 SRR70983673 KM475726 EPI_ISL_436489 Central East LHIN scottbethany@gmail.com 1191 Isabella Street, Unit 70, Campbellford, ON K0L 1L0 Canadore College authorativefigure@nwtha.ca 456 Pleasant Pl, Yellowknife, NT X1A 1O9 2020-05-09 2020-05-28 Canada Nunavut Iqualuit RmYN02 Timor-Leste-Handrail-860 Diagnostic testing Diagnose whether causative agent was SARS-CoV-2 or seasonal influenza. Nucleic acid Convalescent Fluid (pleural) Pleural sac Not Applicable Light switch Animal house Fine Needle Needle Biopsy PantherFusionSARS-CoV-2 Not applicable 293/ACE2 cell line 15 not applicable mRNA (cDNA) Lion Panthera leo Recovered Missing Missing Missing 12 month 0 - 9 Female United States of America nSQu_4 2020-03-05 Ageusia (complete loss of taste); Cough; Headache; Hypotension (low blood pressure) Age 60+; Metastatic disease; Smoking Acute respiratory failure; Guillain-Barré syndrome United States of America New York City New York United States of America 2020-07-14 2020-07-23 Canada, Yellowknife; Canada, Fort Providence: USA, Bismarck Missing Indirect Patient Patient Contact Exposure setting - in the same common room. Cluster investigation Highschool SARS-CoV-2 cluster investigation. Timor-Leste-Handrail-860-1 300 Nextera XT 3225848155 DNBSEQ-G50 NGS protocol v. 12 NGS Libraries NG5T1LK633 Timor-Leste860_2020-02.txt 2020-09-01 Porechop v. 0.2.3 99x timor-leste-handrail-86039assembly.fasta Shovil 91% 17x Timor-Leste860_S1_L001_R1_001.fastq.gz Timor-Leste860_S1_L001_R2_001.fastq.gz /Users/Matthew James/Documents/I./stay dark.fastq.gz /Users/Heather Gonzalez/Downloads/Development$/ Timor-Leste860_2020-02_batch1a.fast5 /Users/Snyder/Downloads/Concern/.fast5 Timor-Leste860_2020-02_batch1a.fasta /Users/Phillip Barry/Desktop/ 185272 2566 21180 601 865.61 MT_419846.1 SARS-CoV-2_MT3989 CASAVA v. 1.8.2 SARS-CoV-2_MT3989.fasta /Users/Jacqueline/Desktop/Work/Seq/Consensus/ Timor-Leste860_2020-02_Annotation-Features.tbl Whole-exome-sequencing-and-bioinformatics-analysis-jhscj6e nsp12 (RdRp) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RdRp nested RT-PCR V.2 13 ORF7b (ns7b) SARS-CoV-2 RT-PCR ORF7b 2020 (Wuhan-ORF1ab; 2019-nCoV-related test version 0.3.0 6 Diana Tucker, Ashley McIntyre, Sandra Smith, Christopher Brown, Robert North, Christopher Green DataHarmonizer provenance: v0.13.7 +NewBrunswick-SARSCoV2-416 SR20-54321 SR20-54320 NewBrunswick-Severeacuterespiratoryvirus2-416 PRJNA623807 PRJNA659224 SAMN14900177 SRR24658112 KY590620 EPI_ISL_461776 Toronto Central LHIN fblack@lhin.on.ca 0000 Bloor Street West, Toronto, Ontario, M6P 1B1 Alberta ProvLab North (APLN) ab3@cdcab.ca 3 Ave SE, Calgary, AB R2E 6K9 2020-06-03 2020-03-11 Canada New Brunswick Moncton RaTG13 NewBrunswick-Severeacuterespiratoryvirus2-416 Surveillance testing The sample was collected to investigate the prevalence of variants associated with mink-to-human transmission in Canada. Swab Convalescent Missing Anus Feces N95 mask Clinical assessment centre Fibrobronchoscope Brush Air filtration Shanghai Bio-Germ Medical Technology Co Ltd Specimens pooled U251 cell line 22 serial passage in heterologous hosts RNA (ribo-depleted) Chicken Gallus gallus Not Collected Not Provided Stable Missing 89 year 80 - 89 Non-binary gender Bosnia and Herzegovina rblyp6 2020-03-08 Confusion; Cough; Pharyngitis (sore throat) Bone marrow failure; Metastatic disease; Cardiac disease Kawasaki disease Japan Montreal Quebec Canada 2020-05-24 2020-05-02 Canada, Alberta; Japan, Tokyo Community Event Direct Other First Nations Reserve Host role - Other: Gardener Diagnostic testing Clinical diagnostic sequencing of confirmed COVID-19 patient. NewBrunswick-Severeacuterespiratoryvirus2-416;3 200 NEBNext Ultra II 5199601997 HiSeq X Ten Seq System Protocol v. 0.1.4 BFX-UT_ARTIC_Illumina V 10.4 BDI5MLQMCI6 NB_SARSCoV2-416_2020ampli.txt 2020-10-20 Deepbinner v. 0.2.0 19x newbrunswick-severeacuterespiratoryvirus2-41628assembly.fasta Canu 20% 15x NB_SARSCoV2-416_S2_L020_R1_001.fasta.gz NB_SARSCoV2-416_S2_L020_R2_001.fasta.gz /Users/Robert/Downloads/unit-/where item.fastq.gz "/Users/Baker/Desktop/""/town-small-consider-wife.fastq.gz" NB_SARSCoV2-416_2020-seq.fast5 /Users/Kim/Google Drive/his/local-method.fast5 NB_SARSCoV2-416_2020-seq.fasta /Users/Stephanie/Downloads/NB_SARSCoV2-416_2020-seq.fasta 219669 3787 12664 1214 831.4 NC_045512.1 ConsensusSeq_U0K724 Carthagene v. 1.2 ConsensusSeq_U0K724.fasta /Users/Haley/Google Drive/ConsensusSeq_U0K724.fasta NB_SARSCoV2-416_2020-seq-AFT.tbl Assessing sequence quality in galaxytrakr v 1.2 ORF7a AllTheTestingPCRing-orf7a v. 2 37 Spike (orf2) 2019-nCoV ORF2-gene-v.10 36 Clyde D. Flores, Tami L. Logan, Amelia M. Foster DataHarmonizer provenance: v0.13.7 +Mali_RmYN02_eaqr SR20-13579 SR20-13575 Mali_RmYN02_eaqr PRJNA623807 PRJNA986922 SAMN16696597 SRR81843993 EU222948 EPI_ISL_518162 BC Centre for Disease Control rSmith@bccdc.ca 655 West 12th Avenue, Vancouver, BC V5Z 4R4 Canada New Brunswick - Vitalité Health Network Heidi-k@brha.ca 295 Mountain Rd, Moncton, NB E1C 2N2 2020-03-04 2020-05-10 Canada Alberta Sikasso Severe acute respiratory syndrome coronavirus 2 Mali_RmYN02_eaqr Missing Missing mRNA (cDNA) Convalescent Fluid Esophagus Sputum Hospital gown School Needle Lumbar Puncture QIAstat-Dx Respiratory SARS-CoV-2 v. 1 RNA re-extraction (post RT-PCR) 293/ACE2 cell line 8 in vivo, TCID RNA (total) Human Homo sapiens Recovered Hospitalized Deceased COVID-19 61 year 60 - 69 Undeclared Kingman Reef GeV:6 2020-01-10 Coma; Dyspnea (breathing difficulty); Rhinorrhea (runny nose) Anemia Abnormal blood oxygen level Canada Dublin Dublin Ireland 2020-10-15 2020-10-30 Canada, New Brunswick Missing Direct Administrator Daycare Direct contact with COVID-19 positive visitor at place of wokr. Research The sample was sequenced to investigate the differences in lineages circulating in Canada during the spring and fall waves of the pandemic. ABC-6543211 260 NEBNext Ultra I 6476849764 Illumina Genome Analyzer II Super Duper Prot. v.1.9 ARTIC Network CO32934396 Mali_RmYN02_eaqr-amplicon.txt 2020-08-31 Guppy v. 0.5.1 116x mali_rmyn02_eaqr1assembly.fasta Velvet 83.65% 111x Mali-RmYN02eaqr_S1_L001_R1_001.fastq.gz Mali-RmYN02eaqr_S1_L001_R2_001.fastq.gz /Users/Lori/Documents/ /Users/Monica Kelley/Google Drive/staff/girl.fastq.gz Mali_RmYN02_eaqr-batch2b.fast5 /Users/Hurley/Downloads/seq/ Mali_RmYN02_eaqr-batch2b.fasta /Users/James/Downloads/be/ 157621 6672 5799 1887 419.92 MN988668 SARS-CoV-2_GWA665 FALCON v0.1 SARS-CoV-2_GWA665.fasta /Users/Watts/Documents/DEN/ Mali_RmYN02_eaqr-annotation.tbl Pacbio long-read sequencing 0.2.6 N (orf9) SARS-CoV-2 real-time RT-PCR N gene 2020 (2019-nCoV-related test) V.2 28 ORF6 (ns6) Withalwaysnote_V 6 6 Margaret Holder DataHarmonizer provenance: v0.13.7 +Newfoundland_Bronchoscope_ISkH SR20-24680 SR20-24670 Newfoundland_Bronchoscope_ISkH PRJNA623807 PRJNA627210 SAMN17946661 SRR58371041 KR120562 EPI_ISL_493706 Eastern Health sshaffer@yahoo.com Health Sciences Centre, Prince Philip Drive, St. John's, NL A1B 3V6 Manitoba Cadham Provincial Laboratory someone@wrha.ca 650 Main St, Winnipeg, MB R3B 1E2 2020-03-06 2020-02-19 Canada Newfoundland and Labrador Stephenville Severe acute respiratory syndrome coronavirus 2 Newfoundland_Bronchoscope_ISkH Not Provided Not Provided RNA Familial Not Applicable Eye Tear Tissue paper Bathroom Collection Cup Necropsy AirSurfaceEnvironmentalProtocol v123 Not applicable Missing 10 ATCC RSV protocol mRNA (cDNA) Human Homo sapiens Not Applicable Not Applicable Recovered COVID-19 84 year 80 - 89 Male Canada 007-Gld-6 2020-02-22 Confusion; Irritability; Cough Hypertension (high blood pressure); Postpartum (≤6 weeks) COVID-19 associated ARDS (CARDS); Cardiac injury; Cardiac arrest Kosovo Nice Provence-Alpes-Cote d'Azur France 2020-09-01 2020-09-03 Canada, Herchmer; Canada, Montreal; Kosovo, Prishtina Not Applicable Unknown First Responder Household Exposure setting - visited personal home for work duty. Surveillance testing Sequence sampled as part of an enhanced COVID-19 surveillance testing initiative that focuses on retirement homes. Newfoundland_Bronchoscope_IskH_007 187 Collibri PS DNA Library Prep Kit 3821789592 Ion Torrent S5 XL pro-seq tech protocol v. 8 NGS protocol v.5.0 LS-2CUO1B Newfoundland_B-IskH_primer_2020-03.txt 2020-10-15 Cutadapt v. 2.10 127x newfoundland_B-IskH_assembly.fasta Canu 56.4% 62x Newfoundland_B-IskH_S1_L103_R1_001.fastq.gz Newfoundland_B-IskH_S1_L103_R2_001.fastq.gz /Users/Nathan Lloyd/Documents/ /Users/Ricky/Google Drive/Window/ Newfoundland_batch03_B-IskH_2020-03.fast5 /Users/Douglas/Google Drive/test/Newfoundland_batch03_B-IskH_2020-03.fast5 Newfoundland_batch03_B-IskH_2020-03.fasta /Users/Sandra English/Desktop/Theory/Newfoundland_batch03_B-IskH_2020-03.fasta 336858 15187 46431 4921 932.78 SRR80285415 Prov_NOJ678 iVar v. 1.0 Prov_NOJ678-consensus.fasta /Users/Mclean/Desktop/-/Prov_NOJ678-consensus.fasta Newfoundland_anno-table_B-IskH_2020-03.tbl Ultra-deep-long-read-nanopore-sequencing-of-mock-m-x9tfr6n nsp15 2019-nCoV nsp 15 v.10 31 ORF1ab (rep) SARS-CoV-2 RT-PCR ORF1ab 2020 (Wuhan-ORF1ab; 2019-nCoV-related test V.3 3 Caleb S. Ribush, Abbie Stanley, Gaston Lafond, Cai Shao, Doreen Wexler, Bonanova Aparicio DataHarmonizer provenance: v0.13.7 +HospitalMissing555 SR20-11111 SR20-10000 HospitalMissing555 PRJNA623807 PRJNA981556 SAMN12616187 SRR32188961 MT752147 EPI_ISL_587439 Northern Health lindseypalmer@northernhealth.ca 299 Victoria St., Prince George, BC V2L 5B8 Public Health Ontario (PHO) rSmith@gmail.com 661 University Ave, Toronto, ON M5G 1M1 2020-02-18 2020-05-17 Canada Manitoba Brandon RaTG13 HospitalMissing555 Missing Missing RNA Acute Not Applicable Intestine Missing Missing Wet market Blood Collection Tube Necropsy CanadaPubHealthLab-SARS-CoV-2_v2.3 Specimens pooled EFK3B cell line 4 in vivo, serial passage Not Applicable Pigeon Columbidae Healthy Missing Deteriorating Missing 86 year 80 - 89 Transgender Saint Helena eEn6 2020-02-13 Cognitive impairment; Fever Lupus; Sickle cell disease Canada Johannesberg Gauteng South Africa 2020-08-08 2020-08-31 Canada, Toronto; USA, New York City Convention Indirect Visitor Community Service Centre Attended convention where multiple people where later diagnosed with COVID-19. Viral passage experiment Study selection of drug-resistant viruses. HospitalMissing555-22 312 QIAseq FX DNA 8439507566 NextSeq 500 ABI xl2500 protocol v. 0.3.5 ABI xl2500 protocol V13 YRPJ-JV6P-HVHT HospitalMissing555_pcr20.txt 2020-10-18 BBTools v. 38.82 129x hospitalmissing55562assembly.fasta SPades 32% 4x HospitalMissing555_S1_L012_R1_001.fastq.gz HospitalMissing555_S1_L012_R2_001.fastq.gz /Users/Henry Moss/Desktop/./ /Users/Brian Cameron/Downloads/form$/light figure degree.fastq.gz HospitalMissing555_sequences.fast5 /Users/Walter Bond/Work/ HospitalMissing555_sequences.fasta /Users/Christopher Martinez/Desktop/administration/ 77793 14795 45791 4145 652.11 NC_045512.1 ConsensusSeq_EAQ565 CASAVA 1.8.2 ConsensusSeq_EAQ565.fasta /Users/Dunlap/Downloads/refgenome/ HospitalMissing555_annotations.tbl Ncov-2019 sequencing protocol for illumina version 3 E (orf4) Severe acute respiratory syndrome coronavirus 2 real-time PCR E gene 2020 v.0.1 4 ORF7a 2019-nCoV orf7a-v. 2 36 Thiery Couture, Xian Ch'iu, G'Kora Zanis DataHarmonizer provenance: v0.13.7 diff 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