Description

Run FastQC on sequenced reads

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.

Output

Name (Type)
Description
Pattern

meta (map)

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

]

html (file)

FastQC report

*_{fastqc.html}

zip (file)

FastQC report archive

*_{fastqc.zip}

versions (file)

File containing software versions

versions.yml
included in
airrflow ampliseq atacseq bacass bamtofastq callingcards chipseq circdna circrna crisprseq cutandrun demo denovotranscript detaxizer fastquorum genomeannotator genomeassembler genomeskim gwas hgtseq hic hicar hlatyping liverctanalysis mag magmap marsseq metaboigniter metatdenovo methylseq nanoseq nascent omicsgenetraitassociation pathogensurveillance phageannotator radseq raredisease readsimulator riboseq rnadnavar rnafusion rnaseq rnasplice rnavar sammyseq sarek scnanoseq scrnaseq seqinspector smrnaseq spatialvi ssds taxprofiler tbanalyzer variantcatalogue viralintegration viralrecon
maintainers
Github user drpatelh
Github user grst
Github user ewels
Github user FelixKrueger
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

fastqc
GPL-2.0-only

FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%A/C/G/T). You get information about adapter contamination and other overrepresented sequences.

bioinformatics.babraham.ac.uk/projects/fastqc bioinformatics.babraham.ac.uk/projects/fastqc/Help