MultiQC protocols

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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



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Publication for MultiQC

MultiQC in pipeline

PMCID: 5428526
PMID: 28529717
DOI: 10.5256/f1000research.12181.r22376

[…] ( ), with gencode m9 annotation for mouse and gencode v22 annotation for human datasets. this pipeline was constructed in bpipe (v0.9.9.3) ( ), and a report summarising the steps produced using multiqc (v0.8) ( )., our gene filtering strategy was identical between datasets. genes that had more than 90% zeroes across all cells, as well as ribosomal and mitochondrial genes, were filtered out. […]

MultiQC in publications

PMCID: 5940186
PMID: 29738525
DOI: 10.1371/journal.pone.0196913

[…] high output running mode. sequencing was performed at the molecular genomics core facility at the university of southern california., 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 […]

PMCID: 5920050
PMID: 29700321
DOI: 10.1038/s41598-018-24701-8

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5807686
PMID: 29459856
DOI: 10.3389/fimmu.2018.00056

[…] 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 […]

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

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Sangram keshari sahu

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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.

Arup Ghosh

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In process of NGS data analysis, lots of statics tics files are generated in each step and merging them is not an easy job. MultiQC is an easy to use command line utility that can merge and generate report from a collection of statistics fro different programs.