Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

sam_clipamplicons

Format

cg sam_clipamplicons ampliconsfile file outfile

Summary

Clip primers from aligned sequences in a sam file (by changing bases to N and quality to 0) given a set of target amplicons

Description

Arguments

ampliconsfile: tab delimited file containing targets with at least following columns: chromosome begin end
file: directory containing reference genomes and variation data
outfile: directory containing reference genomes and variation data

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sam_clipamplicons

Format

Summary

Description

Arguments

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