breseq

docker-breseq

Docker image with breseq software (GitHub page).

breseq

"breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (<20 Mb).". From here.

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Usage

You can download and run this image using the following commands:

# Get Docker image
docker pull ummidock/breseq:0.32.1

# Run sistr_cmd
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/breseq:0.32.1 breseq --reference /data/reference1.gbk --name sample -j 1 --output /data/breseq_out/sample/ /data/sample_1.fastq.gz /data/sample_2.fastq.gz

More examples on how to use breseq (outside a Docker container context) can be found in breseq manual page

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Image Content

This Docker image contains:

• Bowtie2 v2.3.4.1
• R v3.2.3
• breseq v0.32.1

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Citation

If you use breseq in your research, please cite:

Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.

If you use structural variation (junction) predictions, please cite:

Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039.