ChrSexebelari

SNP calling pipeline

SNP calling pipeline to find homozygote SNPs present in JU2817 strain but not in JU2859

Getting Started

These instructions will get you a working version of the pipeline the SNP calling pipeline.

Prerequisites

To run nextflow on you computer you need to have java (>= 1.8) installed.

java --version

To be able to easily test tools already implemented for nextflow on your computer (src/nf_modules/ to see their list). You need to have docker installed.

docker run hello-world

Installing

To install nextflow on you computer simply run the following command:

src/install_nextflow.sh

Then to initialize the necessary Docker tools with the following command:

src/docker_modules/cutadapt/1.14/docker_init.sh
src/docker_modules/UrQt/d62c1f8/docker_init.sh
src/docker_modules/bioawk/1.0/docker_init.sh
src/docker_modules/Bowtie2/2.3.4.1/docker_init.sh
src/docker_modules/sambamba/0.6.7/docker_init.sh
src/docker_modules/sambamba/0.6.7/docker_init.sh
src/docker_modules/GATK/4.0.8.1/docker_init.sh
src/docker_modules/SAMtools/1.7/docker_init.sh
src/docker_modules/bcftools/1.7/docker_init.sh

Necessary R packages

R -e 'install.packages(c("tidyverse", "seqinr"), repos = "https://cloud.r-project.org")'

Running

To launch the analysis, you can execute the content of the script src/1_JU28_59vs17_SNP_calling.sh. There, is a first section to run the pipeline locally with Docker on a training set (after generating the training set), a second to run it with Docker on the full data set, and a last seciton to run it on the PSMN.

Available tools

tool	nf module	docker module	psmn module
BEDtools	ok	ok	ok
BFCtools	no	ok	ok
bioawk	no	ok	ok
Bowtie	ok	ok	no
Bowtie2	ok	ok	ok
BWA	ok	ok	ok
canu	ok	ok	ok
cutadapt	ok	ok	ok
deepTools	no	ok	ok
FastQC	ok	ok	ok
file_handle	no	ok	ok
GATK	no	ok	ok
HISAT2	no	ok	no
HTSeq	ok	ok	ok
Kallisto	ok	ok	ok
MACS2	no	ok	ok
MultiQC	ok	ok	ok
MUSIC	ok	ok	ok
picard	no	ok	ok
pigz	no	ok	ok
RSEM	ok	ok	ok
sambamba	ok	ok	ok
samblaster	ok	ok	ok
SAMtools	ok	ok	ok
SRAtoolkit	ok	ok	ok
Salmon	no	ok	ok
TopHat	no	ok	ok
Trimmomatic	no	ok	ok
UrQt	ok	ok	ok

After running the src/SNP_calling.nf pipeline, the src/intersect_SNP.R R scripts will format the .vcf files into .csv table. The final output is filtered to keep only SNP matching a list of enzymes and SNP that are homozygote in one strain and not present in the other.

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Laurent Modolo - Initial work

See also the list of contributors who participated in this project.

License

This project is licensed under the CeCiLL License- see the LICENSE file for details

LBMC/ChrSexebelari