| Using MultiQC |
| Installation |
Running MultiQC |
Using Reports |
Configuration |
Customising Reports |
Using MultiQC in pipelines |
Downstream analysis |
Common Problems |
installation.md |
usage.md |
reports.md |
config.md |
customisation.md |
pipelines.md |
downstream.md |
troubleshooting.md |
|
| MultiQC Modules |
| Pre-alignment |
Aligners |
Post-alignment |
| Adapter Removal |
AfterQC |
Bcl2fastq |
BioBloom Tools |
Cluster Flow |
Cutadapt |
ClipAndMerge |
FastQ Screen |
FastQC |
Fastp |
FLASh |
Flexbar |
InterOp |
iVar |
Jellyfish |
KAT |
leeHom |
minionqc |
pycoQC |
Pychopper |
SeqyClean |
Sickle |
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/flash.md |
modules/flexbar.md |
modules/interop.md |
modules/ivar.md |
modules/jellyfish.md |
modules/kat.md |
modules/leehom.md |
modules/minionqc.md |
modules/pycoqc.md |
modules/pychopper.md |
modules/seqyclean.md |
modules/sickle.md |
modules/skewer.md |
modules/sortmerna.md |
modules/trimmomatic.md |
|
| Biscuit |
Bismark |
Bowtie 1 |
Bowtie 2 |
BBMap |
HiCUP |
HiCPro |
HISAT2 |
Kallisto |
Long Ranger |
Salmon |
STAR |
TopHat |
DRAGEN |
MALT |
modules/biscuit.md |
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 |
modules/dragen.md |
modules/malt.md |
|
| Bamtools |
Bcftools |
biobambam2 |
BUSCO |
Bustools |
Conpair |
DamageProfiler |
DeDup |
deepTools |
Disambiguate |
featureCounts |
fgbio |
GATK |
goleft_indexcov |
Hap.py |
HiCExplorer |
HOPS |
HOMER |
HTSeq |
JCVI |
Kaiju |
Kraken |
MACS2 |
Methyl QA |
mosdepth |
miRTrace |
mirtop |
MTNucRatio |
MultiVCFAnalyzer |
ngsderive |
OptiType |
phantompeakqualtools |
Peddy |
Picard |
Preseq |
Prokka |
PURPLE |
qc3C |
QoRTs |
Qualimap |
Quast |
RNA-SeQC |
Rockhopper |
RSEM |
RSeQC |
Samblaster |
Samtools |
Sentieon |
Sargasso |
SexDetErrmine |
EigenStratDatabseTools |
Slamdunk |
SnpEff |
SNPsplit |
Somalier |
Supernova |
Stacks |
THeTA2 |
VarScan2 |
VCFTools |
VEP |
verifyBAMID |
modules/bamtools.md |
modules/bcftools.md |
modules/biobambam2.md |
modules/busco.md |
modules/bustools.md |
modules/conpair.md |
modules/damageprofiler.md |
modules/dedup.md |
modules/deeptools.md |
modules/disambiguate.md |
modules/featureCounts.md |
modules/fgbio.md |
modules/gatk.md |
modules/goleft_indexcov.md |
modules/happy.md |
modules/hicexplorer.md |
modules/hops.md |
modules/homer.md |
modules/htseq.md |
modules/jcvi.md |
modules/kaiju.md |
modules/kraken.md |
modules/macs2.md |
modules/methylQA.md |
modules/mosdepth.md |
modules/mirtrace.md |
modules/mirtop.md |
modules/mtnucratio.md |
modules/multivcfanalyzer.md |
modules/ngsderive.md |
modules/optitype.md |
modules/phantompeakqualtools.md |
modules/peddy.md |
modules/picard.md |
modules/preseq.md |
modules/prokka.md |
modules/purple.md |
modules/qc3C.md |
modules/qorts.md |
modules/qualimap.md |
modules/quast.md |
modules/rna_seqc.md |
modules/rockhopper.md |
modules/rsem.md |
modules/rseqc.md |
modules/samblaster.md |
modules/samtools.md |
modules/sentieon.md |
modules/sargasso.md |
modules/sexdeterrmine.md |
modules/eigenstratdatabasetools.md |
modules/slamdunk.md |
modules/snpeff.md |
modules/snpsplit.md |
modules/somalier.md |
modules/supernova.md |
modules/stacks.md |
modules/theta2.md |
modules/varscan2.md |
modules/vcftools.md |
modules/vep.md |
modules/verifybamid.md |
|
|
| Custom Content |
| Introduction |
custom_content.md |
|
| Coding with MultiQC |
| Writing new modules |
Plotting Functions |
MultiQC Plugins |
Writing new templates |
Updating for compatibility |
modules.md |
plots.md |
plugins.md |
templates.md |
compatibility.md |
|
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.
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.