Description

Align reads to multiple reference genomes using fastq-screen

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

database (directory)

fastq screen database folder containing config file and index folders

FastQ_Screen_Genomes

Output

Name (Type)
Description
Pattern

fastq_screen (directory)

Output fastq_screen file containing alignment statistics

*.{_fq_screen}

versions (file)

File containing software versions

versions.yml
maintainers
Github user snesic
Github user JPejovicApis
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

fastqscreen
GPL-3.0-or-later

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

bioinformatics.babraham.ac.uk/projects/fastq_screen stevenwingett.github.io/FastQ-Screen https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip 10.5281/zenodo.5838377