pathogen detection use case example prep

use_case_examples/produce_pathogen_detection_data.sh

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+# Produce Pathogen Detection Toy Dataset
+# This script creates the toy datasets for pathogen detection use case example
+# Make sure SRA tools is in your environment for these use case examples
+
+## Bacterial reads
+# As a naive type dataset would it matter where sample comes from?
+### Download 20 reads from SRR25626360 which represents 20 reads from WGS of Haemophilus influenzae 
+fastq-dump -X 20 -Z SRR25626360 > hinfluenzae_SRR25626360_20reads.fastq
+
+### Download 20 reads from SRR24210460 which represents 20 reads from WGS of mycoplasma pneumoniae from library MDY 
+fastq-dump -X 20 -Z SRR24210460 > mpneumoniae_SRR24210460_20reads.fastq
+
+### Download 20 reads from SRR7217470 which represents 20 reads from WGS of Chlamydia pneumoniae 
+fastq-dump -X 20 -Z SRR7217470 > xpneumoniae_SRR7217470_20reads.fastq
+
+### Download 20 reads from SRR5962942 which represents 20 reads from WGS of Streptococcus pneumoniae 
+fastq-dump -X 20 -Z SRR5962942 > spneumoniae_SRR5962942_20reads.fastq
+
+### Download 20 reads from SRR26202532 which represents 20 reads from WGS of Bordetella pertussis
+fastq-dump -X 20 -Z SRR26202532 > bpertussis_SRR26202532_20reads.fastq
+
+## viral reads
+### Download 20 reads from SRR26589836 sra which represents 20 reads from WGS of covid 
+fastq-dump -X 20 -Z SRR26589836 > sars_cov_2_SRR26589836_20reads.fastq
+
+# Download 100 reads from SRR2830253 which are reads of a healthy human lung microbiome
+fastq-dump -X 100 -Z SRR2830253 > healthy_lung_SRR2830253_100reads.fastq
+
+# download 100 reads from SRR13286708 which is the Lung bacterial microbiome of critical COVID-19
+fastq-dump -X 100 -Z SRR13286708 > critical_COVID_patient_lungs_SRR13286708_100reads.fastq
+
+# Create toy dataset that is tested on a healthy lung fastq reads
+
+# Create toy dataset where fastq reads from either covid or h influenzae are included and use yacht to analyze
+
+# Create a toy dataset that is a referrnce database of known organisms to trigger respiritory disease 

use_case_examples/use-case-examples.md

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+Advantages of using YACHT is that you can analyze from fasta or fastq files.
+
 # Biological Application
 
 Does YACHT provide qunatitative data?
+
 How sensitive is Yacht in detecting viruses?
+
 Could we use YACHT to identify the amount of host DNA?
+
 Is sequencing depth an issue for YACHT?
+
 Can YACHT be used to identify the amount of contamination that there is in a sample?
 
 ## Contamination Detection