Aggregate results from bioinformatics analyses across many samples into a single report

MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

GitHub Python Package Index Documentation Example Report
Quick Install
pip install multiqc    # Install
multiqc .              # Run

Need a little more help? See the full installation instructions.

Ever spent ages collecting reports and wading through log file output?
Here's the answer to your frustrations...

Visualise statistics from your pipeline

MultiQC collects numerical stats from each module at the top the report, so that you can track how your data behaves as it proceeds through your analysis.

View Example Report
General Statistics

Plot all of your samples together

Visualizing your samples together allows detailed comparison, not possible by scanning one report after another.

FastQC GC Overlay Plot

Supports your favourite tools

MultiQC comes supports many common bioinformatics tools out of the box. If you're missing something, just create an issue on GitHub to request it - if you have an example log file it's usually pretty fast.

  • Adapter Removal
  • AfterQC
  • bcl2fastq
  • BioBloom Tools
  • Cluster Flow
  • Cutadapt
  • ClipAndMerge
  • FastQ Screen
  • FastQC
  • Fastp
  • FLASh
  • Flexbar
  • InterOp
  • Jellyfish
  • KAT
  • leeHom
  • minionqc
  • SeqyClean
  • Skewer
  • SortMeRNA
  • Trimmomatic
  • Bismark
  • Bowtie 1
  • Bowtie 2
  • BBMap
  • HiCUP
  • HiC-Pro
  • HISAT2
  • Kallisto
  • Longranger
  • Salmon
  • STAR
  • TopHat
  • Bamtools
  • Bcftools
  • biobambam2
  • Conpair
  • DamageProfiler
  • DeDup
  • deepTools
  • Disambiguate
  • featureCounts
  • Fgbio
  • GATK
  • goleft indexcov
  • HiCExplorer
  • HTSeq
  • MACS2
  • methylQA
  • mosdepth
  • miRTrace
  • MTNucRatio
  • phantompeakqualtools
  • Peddy
  • Picard
  • Preseq
  • Prokka
  • QoRTs
  • Qualimap
  • RNA-SeQC
  • RSEM
  • RSeQC
  • Samblaster
  • Samtools
  • Sargasso
  • Sex.DetErrMine
  • Slamdunk
  • SnpEff
  • Supernova
  • Stacks
  • THeTA2
  • VCFTools
  • VerifyBAMID

Extensible and documented

Want to use this to do something fancy? MultiQC is structured to allow easy extension and customisation with plugin hooks, a submodule framework and simple templating. Everything is well documented, with step by step instructions for writing your new tool.

Read the docs
MultiQC Documentation

Nice things that people have said about MultiQC

See more on →
  • Simple installation
  • Search any directory
  • View report in a web browser
  • Zip file for easy sharing
  • Extensible & well documented

Install from the Python Package Index or Bioconda

To install MultiQC, simply run pip install multiqc on the command line.
If you use conda, you can run conda install -c bioconda multiqc instead.
See the installation instructions for more help.

Documentation View on GitHub View on PyPI