Description

Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fastx:file

Decompressed FASTA/FASTQ input file

*.{fastq,fasta}

Output

name:type
description
pattern

fasta

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}.fasta:file

Collapsed FASTA file

*.fasta

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fastx
AGPL

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

http://hannonlab.cshl.edu/fastx_toolkit http://hannonlab.cshl.edu/fastx_toolkit/commandline https://github.com/agordon/fastx_toolkit
maintainer
Github user jvfe
get in touch
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