Description

A single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

assembly (file)

Draft assembly file

*.{fasta,fastq,gfa}(.gz)?

out_fmt (string)

Output format (fasta, fastq, gfa)

genome_size (integer)

estimated genome size (bp) for NG*.statistics (optional).

target (string)

target specific sequence by header, optionally with coordinates (optional).

agpfile (file)

converts input agp to path and replaces existing paths.

include_bed (file)

generates output on a subset list of headers or coordinates in 0-based bed format.

exclude_bed (file)

opposite of —include-bed. They can be combined (no coordinates).

instructions (file)

set of instructions provided as an ordered list.

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

assembly_summary (file)

Assembly summary statistics file

*.assembly_summary

assembly (file)

The assembly as modified by gfastats

*.{fasta,fastq,gfa}.gz
included in
pairgenomealign
maintainer
Github user mahesh-panchal
get in touch
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Tools