Description

Create read depth histogram and base-level read depth for an assembly based on pacbio data

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

paf_alignment (file)

PAF alignment file

*.paf

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

stat (file)

PacBio Statistic file

*.PB.stat

basecov (file)

PacBio Base coverage file

*.PB.base.cov
maintainer
Github user mahesh-panchal
get in touch
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Tools

purgedups
MIT

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth

github.com/dfguan/purge_dups 10.1093/bioinformatics/btaa025