Description

Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted.

Input

name:type
description
pattern

meta{:bash}

:map

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

graph{:bash}

:file

Pangenome graph in GFA v1.0 format or in ODGI binary format

*.{gfa,og}

Output

name:type
description
pattern

lay{:bash}

meta{:bash}

:map

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

*.lay{:bash}

:file

File containing a 2D layout of a pangenome graph in a binary format. Usually ends with ‘.lay’. Optional output specified by the --out FILE argument. Either this or the TSV layout output must be specified.

*.{lay}

tsv{:bash}

meta{:bash}

:map

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

*.tsv{:bash}

:file

File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the --tsv FILE argument. Either this or the binary layout output must be specified.

*.{tsv}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
pangenome
maintainer
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