Description

Common transformation operations on FASTA or FASTQ files.

Input

Name (Type)
Description
Pattern

meta (map)

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

sequences (file)

A FASTQ or FASTA file

*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

sequences (file)

FASTQ/FASTA file containing renamed sequences

*.{fastq.gz, fasta.gz}
included in
crisprseq radseq
authors
Github user hseabolt Github user mjcipriano Github user sateeshperi
get in touch
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Tools

seqtk
MIT

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.

github.com/lh3/seqtk docs.csc.fi/apps/seqtk https://github.com/lh3/seqtk