Description

Common transformation operations on FASTA or FASTQ files.

Input

name:type
description
pattern

meta{:bash}

:map

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

fastx{:bash}

: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

fastx{:bash}

meta{:bash}

:map

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

*.gz{:bash}

:file

FASTQ/FASTA file containing renamed sequences

*.{fastq.gz, fasta.gz}

versions_seqtk{:bash}

${task.process}{:bash}

:string

The name of the process

seqtk{:bash}

:string

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

seqtk{:bash}

:string

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p'{:bash}

:eval

The expression to obtain the version of the tool

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
included in
crisprseqmetatdenovoradseq
maintainers
Github user hseabolt
Github user mjcipriano
Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub