Description

Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fastx (file)

Sequence file in fasta/q format

*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]

Output

Name (Type)
Description
Pattern

meta (map)

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

]

text (file)

Text file in tabular format

*.txt[.gz,.zstd,.zst]

versions (file)

File containing software versions

versions.yml
maintainer
Github user heuermh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

seqkit
MIT

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.

github.com/shenwei356/seqkit bioinf.shenwei.me/seqkit 10.1371/journal.pone.0163962