Containers for Bioinformatics Workflows

Usage guidelines

1. cutadapt

cutadapt documentation

docker run --entrypoint cutadapt -v <path to data folder>:/data pskolekar/cutadapt:2.9 -u 17 -o /data/test_trimmed_R1.fastq.gz /data/test_R1.fastq.gz

2. bam-readcount

bam-readcount documentation

docker run -it -v <path to data folder>:/data pskolekar/bam-readcount:latest bam-readcount -f <ref.fa> <some.bam>

3. FastQC

FastQC documentation

 docker run -it pskolekar/fastqc:latest fastqc --help  

4. BSMAP

BSMAP documentation

 docker run -it pskolekar/bsmap:latest bsmap -h
 docker run -it pskolekar/bsmap:latest methratio.py -h

5. samtools

Samtools documentation

 docker run -it pskolekar/samtools:latest samtools