seqtk_seq

Description¶

Common transformation operations on FASTA or FASTQ files.

Keywords: seq, fasta, fastq

Installation¶

ebi-metagenomics/seqtk/seq

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install seqtk/seq

Tools¶

seqtk¶

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.

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}`