Description

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

Input

Name (Type)
Description
Pattern

meta (map)

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

]

gfa (file)

Variation graph in GFA 1.0 format

*.{gfa}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

gfa (file)

Linearized and simplified graph in GFA 1.0 format

*.smoothxg.{gfa}

versions (file)

File containing software versions

versions.yml

maf (file)

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

*.{maf}
included in
pangenome
author
Github user heuermh, @subwaystation
get in touch
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Tools

smoothxg
MIT

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

github.com/pangenome/smoothxg