Description

Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file

Input

name:type
description
pattern

meta:map

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

gfa:file

GFA file containing a graph without overlapping nodes

*.gfa

bed_subset:file

Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph

*.{txt, bed}

bed_exclude:file

Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths

*.{txt, bed}

tsv_groupby:file

Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged

*.{txt, bed}

Output

name:type
description
pattern

tsv

meta:map

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

*.{tsv, html}:file

TSV file containing the statistics. Alternatively, the HTML file can be the output

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

panacus
MIT

panacus is a tool for computing counting statistics for GFA files