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 (map)

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

]

graph (file)

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

*.{gfa,og}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

lay (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 (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}
included in
pangenome
author
Github user subwaystation
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Tools

odgi
MIT

An optimized dynamic genome/graph implementation

github.com/pangenome/odgi odgi.readthedocs.io/en/latest https://github.com/pangenome/odgi 10.1093/bioinformatics/btac308