pegi3s/bowtie1 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 Bowtie 1⁠, an ultrafast, memory-efficient short read aligner.

To see the Bowtie 1⁠ help, just run docker run --rm pegi3s/bowtie1 bowtie --help.

⁠Using the Bowtie image in Linux

⁠Build a genome index

You should adapt and run the following command:

docker run --rm -v /your/data/dir:/data pegi3s/bowtie1 \
	sh -c "mkdir /data/bwt1_index \
	&& bowtie-build /data/genome.fna /data/bwt1_index/built_index"

In this commands, you should replace:

• /your/data/dir to point to the directory that contains the input file/files you want to process.
• genome.fna to the name of the fastq file with the genome from which the index is built.

⁠Align

You should adapt and run the following command:

docker run --rm -v /your/data/dir:/data pegi3s/bowtie1 bowtie -S /data/bwt1_index/built_index /data/input.fq /data/output.sam

In this commands, you should replace:

• /your/data/dir to point to the directory that contains the input file/files you want to process.
• built_index to the root name of the genome index files, e.g.: index.1.ebwt, index.2.ebwt... --> index. Do not change this if you used the previous command to build the genome index.
• input.fq to the actual name of the input file/files you want to process, use colons or regex for align to several files.
• output.sam the actual name of your output file.

⁠Test data

To test the previous commands, you can download the following files:

• genome⁠ (12MB). The genome is compressed in .gz and needs to be extracted before use.
• fastq data⁠ (3.5MB). The data is compressed in .gz and needs to be extracted before use.

To test the first command you need to download the genome and replace /data/genome.fna to /data/GCF_000146045.2_R64_genomic.fna.

To test the second command (after executing the first one), you need to download the fastq data and to replace /data/input.fq with /data/GSM2527046_AG1GY_128nM_SAM_offset0_0_NeighborhoodMapping_R1_001.fastq.