Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

paf_alignment{:bash}

:file

PAF alignment file

*.paf

Output

name:type
description
pattern

stat{:bash}

meta{:bash}

:map

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

*.PB.stat{:bash}

:file

PacBio Statistic file

*.PB.stat

basecov{:bash}

meta{:bash}

:map

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

*.PB.base.cov{:bash}

:file

PacBio Base coverage file

*.PB.base.cov

versions_purgedups{:bash}

${task.process}{:bash}

:string

The name of the process

purge_dups{:bash}

:string

The name of the tool

1.2.6{:bash}

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

purge_dups{:bash}

:string

The name of the tool

1.2.6{:bash}

:string

The expression to obtain the version of the tool

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
maintainer
Github user mahesh-panchal
get in touch
Ask a question on Slack Open an issue on GitHub