Description

Select sequences from a large file based on name/ID

Input

name:type
description
pattern

meta:map

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

sequence:file

Fasta or fastq file containing sequences to be filtered

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

pattern:file

pattern file (one record per line). If no pattern is given, a string can be specified within the args using ‘-p pattern_string’

*.{txt,tsv}

Output

name:type
description
pattern

filter

meta:map

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

*.{fa,fq}.gz:file

Fasta or fastq file containing the filtered sequences

*.{fa,fq}[.gz]

versions

versions.yml:file

File containing software versions

versions.yml

Tools

seqkit
MIT

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