modules/purgedups_pbcstat

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

sortgenome assemblypurge duplicationsread depth

https://github.com/nf-core/modules/[...]/modules/nf-core/purgedups/pbcstat

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

`stat`

`meta:map`

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

]

`*.PB.stat:file`

PacBio Statistic file

*.PB.stat

`basecov`

`meta:map`

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

]

`*.PB.base.cov:file`

PacBio Base coverage file

*.PB.base.cov

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/purgedups_pbcstat

Description

Input

`meta:map`

`paf_alignment:file`

Output

`stat`

`meta:map`

`*.PB.stat:file`

`basecov`

`meta:map`

`*.PB.base.cov:file`

`versions`

`versions.yml:file`

Tools

purgedups
MIT

maintainer

get in touch

modules/purgedups_pbcstat

Description

Input

meta:map

paf_alignment:file

Output

stat

meta:map

*.PB.stat:file

basecov

meta:map

*.PB.base.cov:file

versions

versions.yml:file

Tools

purgedups MIT

maintainer

get in touch

`meta:map`

`paf_alignment:file`

`stat`

`meta:map`

`*.PB.stat:file`

`basecov`

`meta:map`

`*.PB.base.cov:file`

`versions`

`versions.yml:file`

purgedups
MIT