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

]

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 specificied within the args using ‘-p pattern_string’

*.{txt,tsv}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

filter (file)

Fasta or fastq file containing the filtered sequences

*.{fa,fq}[.gz]
author
Github user Joon-Klaps
get in touch
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Tools

seqkit
MIT

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

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