Description

Linearize and simplify variation graph in GFA format using blocked partial order alignment

Input

name:type
description
pattern

meta{:bash}

:map

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

gfa{:bash}

:file

Variation graph in GFA 1.0 format

*.{gfa}

Output

name:type
description
pattern

gfa{:bash}

meta{:bash}

:map

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

*smoothxg.gfa{:bash}

:file

Linearized and simplified graph in GFA 1.0 format

*.smoothxg.{gfa}

maf{:bash}

*.maf{:bash}

:file

write the multiple sequence alignments (MSAs) in MAF format in this file (optional)

*.{maf}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

smoothxg
MIT

smoothxg linearizes and simplifies variation graphs using blocked partial order alignment.

github.com/pangenome/smoothxg
included in
pangenome
maintainer
Github user heuermh, @subwaystation
get in touch
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