docker-bwa

BWA mapping tools and samtools

Installation

docker pull quay.io/refgenomics/docker-bwa
docker run  quay.io/refgenomics/docker-bwa

The align convenience command

Included in this docker container is the align.py convience pipeline. This script integrates the indexing, mapping, and sam->sorted bam output in one command. align can be invoked by running the align command in the container:

$ docker run quay.io/refgenomics/docker-bwa align

Usage and help is available:

$ docker run quay.io/refgenomics/docker-bwa align --help
usage: align [-h] [-b | -s] [-o OUT] [--verbose]
             references [references ...] reads

positional arguments:
  references         Reference FASTA file(s) used for alignment
  reads              Reads FASTA or FASTQ file to be aligned

optional arguments:
  -h, --help         show this help message and exit
  -b, --bam          Output a bam file
  -s, --sam          Output a bam file
  -o OUT, --out OUT  Output file or destination (default is stdout)
  --verbose          Output stderr from commands

As an example, you can quickly align a set of reads to a fasta file like so:

docker run -v ~/local:/data quay.io/refgenomics/docker-bwa align \
    data/genome.fa \
    /data/reads.fa --sam

An the resuling sam file will be output to stdout.

To create a sorted bam file (and index):

docker run -v ~/local:/data quay.io/refgenomics/docker-bwa align \
    data/genome.fa \
    /data/reads.fa --bam \
    --out /data/output.bam

Bonus tip: With a simple bash function, the above workflow can be further simplified:

$ function d() { docker run -v `pwd`:/data quay.io/refgenomics/$@; }
$ d docker-bwa align /data/genome.fa /data/reads.fa

Available binaries

BWA

This image contains BWA-mem v0.7.10. To run:

docker run quay.io/refgenomics/docker-bwa bwa [bwa-options]

Samtools

This image contains samtools 0.1.19-96b5f2294a. To run:

docker run quay.io/refgenomics/docker-bwa samtools [samtools-options]

Copyright and License

MIT License, see LICENSE for details.

Copyright (c) 2014 One Codex, Nik Krumm, and contributors.