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.
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
breseq-rm-bg v0.2.1 is tested for breseq version 0.33.2, it should works for recent breseq versions.