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Removing control/background mutations from breseq output index.html
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README.md

breseq-rm-bg

This tools is used for finding mutations using breseq for experiments with control/background samples.

If you use breseq to find mutation in bacteria, but the reference strain is not well assembled or annotated, you should re-seq your reference strain as a control/background, and use a close strain as reference for analysis.

breseq-rm-bg makes breseq output file (output/index.html) more readable by removing mutations that are in control/background sample.

Download

Executable binary files.

Usage

breseq-rm-bg --bg-inter --bg-files bg1/output/index.html ---bg-files bg2/output/index.html \
  sample1/output/index.html > sample1/output/index.filtered.html

Compatibility

breseq-rm-bg v0.2.0 is tested for breseq version 0.33.2, it should works for recent breseq versions.

License

MIT License

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