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

meta (map)

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

versions (file)

File containing software versions

versions.yml

fasta (file)

Collapsed FASTA file

*.fasta
maintainer
Github user jvfe
get in touch
Ask a question on Slack Open an issue on GitHub

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