Description

Sort fasta entries by decreasing abundance (—sortbysize) or sequence length (—sortbylength).

Input

Name (Type)
Description
Pattern

meta (map)

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

fasta (file)

Sequences to be sorted in FASTA format

*.{fasta,fa,fasta.gz,fa.gz}

sort_arg (string)

Argument to provide to sort algorithm. Sort by abundance with —sortbysize or by sequence length with —sortbylength.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

fasta (file)

Sorted FASTA file

*.{fasta}

versions (file)

File containing software versions

versions.yml
included in
crisprseq
maintainer
Github user mirpedrol
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

vsearch
GPL v3-or-later OR BSD-2-clause

VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)

github.com/torognes/vsearch github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf https://github.com/torognes/vsearch 10.7717/peerj.2584