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modules
README.md
compatibility.md
config.md
custom_content.md
customisation.md
installation.md
modules.md
plots.md
plugins.md
reports.md
templates.md
troubleshooting.md
usage.md

README.md

Using MultiQC MultiQC Modules Custom Content Coding with MultiQC
Installation Running MultiQC Using Reports Configuration Customising Reports Common Problems
installation.md
usage.md
reports.md
config.md
customisation.md
troubleshooting.md
Pre-alignment Aligners Post-alignment
Adapter Removal AfterQC Bcl2fastq BioBloom Tools Cluster Flow Cutadapt ClipAndMerge FastQ Screen FastQC Fastp Flexbar InterOp Jellyfish KAT leeHom Skewer SortMeRNA Trimmomatic
modules/adapterRemoval.md
modules/afterqc.md
modules/bcl2fastq.md
modules/biobloomtools.md
modules/clusterflow.md
modules/cutadapt.md
modules/clipandmerge.md
modules/fastq_screen.md
modules/fastqc.md
modules/fastp.md
modules/flexbar.md
modules/interop.md
modules/jellyfish.md
modules/kat.md
modules/leehom.md
modules/skewer.md
modules/sortmerna.md
modules/trimmomatic.md
Bismark Bowtie 1 Bowtie 2 BBMap HiCUP HiCPro HISAT2 Kallisto Long Ranger Salmon STAR TopHat
modules/bismark.md
modules/bowtie1.md
modules/bowtie2.md
modules/bbmap.md
modules/hicup.md
modules/hicpro.md
modules/hisat2.md
modules/kallisto.md
modules/longranger.md
modules/salmon.md
modules/star.md
modules/tophat.md
Bamtools Bcftools BUSCO Conpair Disambiguate DeDup deepTools featureCounts GATK goleft_indexcov Hap.py HiCExplorer HOMER HTSeq MACS2 Methyl QA miRTrace Peddy Picard Preseq Prokka QoRTs Qualimap Quast RNA-SeQC RSEM RSeQC Samblaster Samtools Sargasso Slamdunk SnpEff Supernova THeTA2 VCFTools verifyBAMID
modules/bamtools.md
modules/bcftools.md
modules/busco.md
modules/conpair.md
modules/disambiguate.md
modules/dedup.md
modules/deeptools.md
modules/featureCounts.md
modules/gatk.md
modules/goleft_indexcov.md
modules/happy.md
modules/hicexplorer.md
modules/homer.md
modules/htseq.md
modules/macs2.md
modules/methylQA.md
modules/mirtrace.md
modules/peddy.md
modules/picard.md
modules/preseq.md
modules/prokka.md
modules/qorts.md
modules/qualimap.md
modules/quast.md
modules/rna_seqc.md
modules/rsem.md
modules/rseqc.md
modules/samblaster.md
modules/samtools.md
modules/sargasso.md
modules/slamdunk.md
modules/snpeff.md
modules/supernova.md
modules/theta2.md
modules/vcftools.md
modules/verifybamid.md
Introduction
custom_content.md
Writing new modules Plotting Functions MultiQC Plugins Writing new templates Updating for compatibility
modules.md
plots.md
plugins.md
templates.md
compatibility.md

Welcome!

MultiQC Documentation

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It's written in Python and contains modules for a number of common tools.

The documentation has the following pages:

These docs can be read in any of three ways:

If you're curious how the website works, check out the MultiQC website repository.

Contributing to MultiQC

If you write a module which could be of use to others, it would be great to merge those changes back into the core MultiQC project.

For instructions on how best to do this, please see the contributing instructions.