MultiQC statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


MultiQC specifications


Unique identifier OMICS_12426
Name MultiQC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.7
Stability Stable
Index, Bioconda
Source code URL
Maintained Yes




No version available



Publication for MultiQC

MultiQC citations


Optimizing exosomal RNA isolation for RNA Seq analyses of archival sera specimens

PLoS One
PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913
call_split See protocol

[…] Raw data were downloaded as FASTQ files and QC performed using MultiQC []. Around 10 million reads were generated for each sample. The raw data was pre-processed using Trimgalore version 0.4.2 [] to remove Illumina adapters and reads shorter than 20 bp. Trimmed r […]


A compendium of long non coding RNAs transcriptional fingerprint in multiple myeloma

Sci Rep
PMCID: 5920050
PMID: 29700321
DOI: 10.1038/s41598-018-24701-8
call_split See protocol

[…] procedure. Differentially expressed genes were identified using DeSeq at FDR < 0.01, provided that expression across the whole dataset was not null. Quality Control (QC) analysis was performed using multiqc tool and the QC metrics were comparable for all samples. The annotation allowed to detect 14,202 lncRNAs, including the following Gencode biotypes: lincRNA, antisense, bidirectional promoter l […]


De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] kb, median size: ~3 kb, adaptor length: 38 bp).Pre-quality check report was generated using the String Graph Assembler software package and quality metrics before assembly with both FastQC as well as MultiQC. These analyses revealed that 91% of sequences had a mean Phred quality score >=30, 96% a mean Phred quality score >=30 and 39% of sequences had an adapter sequence (either Illumina or Nextera […]


Integrated transcriptomes throughout swine oestrous cycle reveal dynamic changes in reproductive tissues interacting networks

Sci Rep
PMCID: 5882957
PMID: 29615657
DOI: 10.1038/s41598-018-23655-1

[…] 025.4) and transcriptome (Ensembl v78) from the Ensembl genome browser ( by tophat2 v2.0.13 using the default options. Mapping statuses were plotted and analysed by MultiQC v0.8dev. All possible transcripts were inferred using the Reference Guided Transcriptome Assembly (RABT) mode in cufflinks v2.2.1. The gene expression level was obtained using the measurement […]


The Immune and Non Immune Pathways That Drive Chronic Gastrointestinal Helminth Burdens in the Wild

Front Immunol
PMCID: 5807686
PMID: 29459856
DOI: 10.3389/fimmu.2018.00056
call_split See protocol

[…] quality-checked using FastQC v. 0.11.5 () and sequences of low-quality and sequencer adapters trimmed using cutadapt v. 1.14 (). The resulting trimmed reads were then quality-checked using FastQC and MultiQC () as above (see MultiQC report in Supplementary Data Sheet 1), and aligned to a reference transcriptome and quantified using Kallisto v. 0.43.1 (). An A. sylvaticus transcriptome generated fr […]


In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

PMCID: 5784243
PMID: 29404412
DOI: 10.1128/mSphere.00517-17

[…] okka annotation pipeline v. 1.1.12b () using the E24377A (CP000800.1) ETEC proteome as primary annotation source. Summary statistics from the sequencing, assembly, and annotation were collected using MultiQC v1.0 () and are shown in (PacBio) and (Illumina) in the supplemental material. […]


Looking to check out a full list of citations?

MultiQC institution(s)
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Science for Life Laboratory, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden; Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, Stockholm, Sweden
MultiQC funding source(s)
This work was supported by the Science for Life Laboratory and the National Genomics Infrastructure, NGI.

MultiQC reviews

star_border star_border star_border star_border star_border
star star star star star
Anamaria Elek's avatar image No country

Anamaria Elek

star_border star_border star_border star_border star_border
star star star star star
Easily creates intuitive and annotated plots from FastQC and FastQ Screen reports for multiple samples.

Sangram keshari sahu

star_border star_border star_border star_border star_border
star star star star star
One tool for many QC report solutions. Many of the bioinformatics tools generate a statistics file at the end of the analysis, but the quick visualisation for interpretation purpose is a challenging task for many. This MultiQC tool does a great job by generating data figures in an HTML report file with use of a single command. It automatically detects the tool information. The development team behind is very active by updating new tools to its list.