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

meta (map)

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

versions (file)

File containing software versions

versions.yml

tsv (file)

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

*.tsv

html (file)

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

*.html
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Github user subwaystation
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Tools

panacus
MIT

panacus is a tool for computing counting statistics for GFA files

github.com/marschall-lab/panacus