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

assembly_summary

meta:map

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

]

*.assembly_summary:file

Assembly summary statistics file

*.assembly_summary

assembly

meta:map

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

]

*.${out_fmt}.gz:file

The assembly as modified by gfastats

*.{fasta,fastq,gfa}.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
pairgenomealign
maintainer
Github user mahesh-panchal
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