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{:bash}

:map

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

gfa{:bash}

:file

GFA file containing a graph without overlapping nodes

*.gfa

bed_subset{:bash}

: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{:bash}

: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{:bash}

: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{:bash}

meta{:bash}

:map

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

*.{tsv, html}{:bash}

:file

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

*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

panacus
MIT

panacus is a tool for computing counting statistics for GFA files

github.com/marschall-lab/panacus
maintainers
Github user heringerp
Github user subwaystation
get in touch
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