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Plot mutations and read coverage in bacterial genomes

Hi all,

I'm working with breseq to identify all kinds of mutations in bacterial genomes, and I would like to know if there is a tool or R package that can plot the coverage along with the mutations across the entire bacterial chromosome.

I have been using Integrative Genomics Viewer (IGV) to visualize mutations and coverage from BAM files, but the figures don't look very good (especially for publication) so I'm looking for any possible recommendations.

Thanks,

plot mutations coverage sequencing r
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updated by colindaven colindaven • written by Paul • Paul

1 answer

Here's "a few" others in a rather excellent and exhaustive list from cmdcolin - https://cmdcolin.github.io/awesome-genome-visualization/?latest=true

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written by colindaven colindaven

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