pegi3s/bwa repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of BWA⁠, a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the remaining two for 70bp to 1Mbp sequences. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

To see BWA options, just run docker run --rm pegi3s/bwa bwa.

⁠Using the BWA image in Linux

You should adapt and run the following command: docker run --rm -v "/your/data/dir:/data" pegi3s/bwa bwa <command> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTA file you want to analyze.
• <command> with the specific command of the BWA tool.
• <options> with the specific options of the BWA tool. These options will include the input/output files, which should be referenced under /data/.

For instance, if you want to align with the BWA-MEM algorithm the reads 7859_GPI.read1.fq and 7859_GPI.read2.fq with the chromosome chr19_KI270866v1_alt.fasta, you should run: docker run --rm -v "/your/data/dir:/data" pegi3s/bwa bwa mem /data/chr19_KI270866v1_alt.fasta /data/7859_GPI.read1.fq /data/7859_GPI.read2.fq > aln-pe.sam

⁠Note

Before executing the previous command, it is necessary to generate the index files of the sequence chr19_KI270866v1_alt.fasta. To do so, you should run: docker run --rm -v "/your/data/dir:/data" pegi3s/bwa bwa index /data/chr19_KI270866v1_alt.fasta

⁠Test data

To test the previous commands, the input FASTA file used is available here⁠. The two FASTQ files used, one for each mate of the paired reads, are available here⁠ and here⁠.

⁠Using the BWA image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/bwa bwa <command> <options>