NorwegianVeterinaryInstitute · evezeyl · Mar 19, 2019 · Mar 22, 2019 · Mar 22, 2019 · Mar 22, 2019
diff --git a/PlasmidFinder.md b/PlasmidFinder.md
@@ -0,0 +1,40 @@
+**PlasmidFinder**
+-------------------------
+PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/plasmidfinder/src
+
+#### For further reading
+https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068535/ 
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+# Activate Conda environment 
+conda activate PlasmidFinder
+
+# Database location
+DB="/work/projects/nn9305k/src/PlasmidFinder/PlasmidFinder_DB/plasmidfinder_db/"
+
+# Note: Dont need to mention the BLAST location
+python /work/projects/nn9305k/src/PlasmidFinder/plasmidfinder/plasmidfinder.py -p $DB -i input_file -o output_file
+
+# deactivate Conda environment 
+conda deactivate
+```
diff --git a/PointFinder.md b/PointFinder.md
@@ -0,0 +1,34 @@
+**Executing PointFinder**
+-------------------------
+The tool detects chromosomal mutations predictive of drug resistance based on WGS data.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/pointfinder
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate PointFinder
+
+# Database location
+PointFinder_DB="/work/projects/nn9305k/src/PointFinder_DB/src/"
+python PointFinder.py -p $PointFinder_DB -i input_file -o output_file
+
+conda deactivate 
+```
diff --git a/README.md b/README.md
@@ -20,6 +20,7 @@ The instructors are:
 
   * [Use of mash](mash.md)
   * [Use of conda](conda.md)
+  * [Mapping and visualization](assembly_visualization.md)
 
 
 ## Course pages

diff --git a/R_trees.md b/R_trees.md
@@ -0,0 +1,16 @@
+start with data prep
+
+# Data: 
+
+
+# Required R packages:
+`distanceR`
+`ggtree`
+
+
+# make a simple tree with just labels
+
+# Add decorations
+
+each step has to build on the previous one
+but you need to get something on screen, very fast
diff --git a/ResFinder.md b/ResFinder.md
@@ -0,0 +1,38 @@
+**Executing ResFinder** 
+----------------------
+Use the below code to execute ResFinder Abel. Dont need to mention BLAST location.
+Contact Jeevan if you have any issues. 
+
+PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/pointfinder
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate ResFinder 
+
+# Location of PointFinder DB
+PF_DB="/work/projects/nn9305k/src/ResFinder/ResFinderDB/src/"
+
+python /work/projects/nn9305k/src/ResFinder/src/resfinder.py -i <Input File> -p /work/projects/nn9305k/src/ResFinder/ResFinderDB/src/ -k /work/projects/nn9305k/src/kma/ -o Output
+
+conda deactivate
+```
diff --git a/SeqSero.md b/SeqSero.md
@@ -0,0 +1,33 @@
+**Excuting SeqSero**
+--------------------
+SeqSero is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. 
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://github.com/denglab/SeqSero 
+
+#### For further reading
+http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15 
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate SeqSero_Shared
+python /work/projects/nn9305k/src/SeqSero/SeqSero/SeqSero.py -m "1" -i input_file -b "mem"
+conda deactivate 
+```
diff --git a/SeroTypeFinder.md b/SeroTypeFinder.md
@@ -0,0 +1,32 @@
+**Executing SeroTypeFinder**
+============================
+SerotypeFinder identifies the serotype in total or partial sequenced isolates of E. coli.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/serotypefinder/src/master/
+
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate SeroTyperFinder
+DB=/work/projects/nn9305k/src/SeroTypeFinder/serotypefinder_db/
+python /work/projects/nn9305k/src/SeroTypeFinder/serotypefinder.py -i input_file -o output -p $DB -mp /work/projects/nn9305k/src/kma/kma
+conda deactivate 
+```
diff --git a/ShigaTyper.md b/ShigaTyper.md
@@ -0,0 +1,33 @@
+**ShighaTyper**
+---------------
+ShigaTyper is a quick and easy tool designed to determine Shigella serotype using Illumina paired end reads with low computation requirement.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/plasmidfinder/src
+
+#### For further reading
+https://aem.asm.org/content/85/7/e00165-19
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate ShigaTyper
+python /work/projects/nn9305k/src/ShigaTyper/shigatyper/shigatyper.py Read1 Read2 -n sample_name 
+conda deactivate 
+```
diff --git a/VirulanceFinder.md b/VirulanceFinder.md
@@ -0,0 +1,36 @@
+**Executing VirulanceFinder**
+-----------------------------
+VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/virulencefinder
+
+#### For further reading
+https://www.ncbi.nlm.nih.gov/pubmed/24574290
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+module load Miniconda3/4.4.10
+
+# Activate Conda environment 
+conda activate VirulanceFinder
+DB="/work/projects/nn9305k/src/VirulanceFinder/Virulance_DB/virulencefinder_db"
+python /work/projects/nn9305k/src/VirulanceFinder/src/virulencefinder.py -p $DB 
+conda deactivate
+```
diff --git a/assembly_visualization.md b/assembly_visualization.md
@@ -16,10 +16,7 @@ Usually few mismatches are allowed (think about the consequences).
 
 Reads can be mapped as paired or single. If paired is used, then the matching regions are defined by the insert size and the length of each read
 
-<p align="center">
-<a href="https://commons.wikimedia.org/wiki/File:Mapping_Reads.png"> <img src="https://upload.wikimedia.org/wikipedia/commons/2/2e/Mapping_Reads.png" width="400">
-<br>
-</p>
+![https://commons.wikimedia.org/wiki/File:Mapping_Reads.png](https://upload.wikimedia.org/wikipedia/commons/2/2e/Mapping_Reads.png)
 
 ### 1.2 Why mapping reads
 
@@ -170,10 +167,7 @@ In `Bifrost` we annotated the assembly with `Prokka` (using annotations derived
 
 ## 2.4 Loading files in [IGV](https://software.broadinstitute.org/software/igv/)
 
-<p align="center">
-<img src="./figures/IGV.png">
-<br>
-</p>
+![IGV](./figures/IGV.png)
 
 1. Create a `genome file` this allows associating tracks to the assembly : `Genomes > create.genome file`. Use the menu to select your assembly file `.fasta`and the annotation-gene file: `.gff`
 

diff --git a/figures/poppunk/2DGMM_fit.png b/figures/poppunk/2DGMM_fit.png
diff --git a/figures/poppunk/2DGMM_fit_DPGMM_fit.png b/figures/poppunk/2DGMM_fit_DPGMM_fit.png
diff --git a/figures/poppunk/2DGMM_fit_distanceDistribution.png b/figures/poppunk/2DGMM_fit_distanceDistribution.png
diff --git a/figures/poppunk/2DGMM_refine_refined_fit.png b/figures/poppunk/2DGMM_refine_refined_fit.png
diff --git a/figures/poppunk/DBSCAN_fit_dbscan.png b/figures/poppunk/DBSCAN_fit_dbscan.png
diff --git a/figures/poppunk/poppunk_random_k.png b/figures/poppunk/poppunk_random_k.png
diff --git a/figures/poppunk/refine_poppunk.png b/figures/poppunk/refine_poppunk.png
diff --git a/pMLST.md b/pMLST.md
@@ -0,0 +1,38 @@
+**Executing pMLST** 
+----------------------
+Use the below code to execute pMLST in Abel. 
+
+pMLST enables investigators to determine the ST based on WGS data.
+
+Contact Jeevan in slack if you have any issues or further assistance (F. ex. run the tool for multiple isolates).
+
+#### User Manual 
+https://bitbucket.org/genomicepidemiology/pmlst/src 
+
+#### Here is the EXAMPLE SLURM script for Abel to excute the tool.
+Important rules to follow
+* Refer the user manual for all the parameters in the tool
+* Keep your data in /project/nn9305k/
+* Store your resutls also in /project/nn9305k/
+* Execute the script from your home directory
+
+```
+#!/bin/bash
+#SBATCH --job-name=DontKillMe
+#SBATCH --account=nn9305k
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=32G
+
+## Set up job environment:
+source /cluster/bin/jobsetup
+
+conda activate pMLST
+
+# Location of pMLST DB
+pMLST_DB="/work/projects/nn9305k/src/pMLST/pMLST_DB/pmlst_db/"
+
+python3 /work/projects/nn9305k/src/pMLST/src/pmlst.py -i <Input File> -p $pMLST_DB -o Output
+
+conda deactivate
+```
+