Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Sequences to be sorted in FASTA format

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

sort_arg{:bash}

:string

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

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

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

*.fasta{:bash}

:file

Sorted FASTA file

*.{fasta}

versions_vsearch{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

vsearch{:bash}

:string

The tool name

vsearch --version 2>&1 | sed -n "1s/.*v\([0-9.]*\).*/\\1/p"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

vsearch{:bash}

:string

The tool name

vsearch --version 2>&1 | sed -n "1s/.*v\([0-9.]*\).*/\\1/p"{:bash}

:eval

The expression to obtain the version of the tool

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
included in
crisprseq
maintainer
Github user mirpedrol
get in touch
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