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MGmapper specifications


Unique identifier OMICS_18201
Name MGmapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Single or paired-end reads
Input format FASTQ
Output data Performs sequence mapping and taxonomy annotation.
Output format BAM, TXT, XLS
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Thomas Sicheritz Pontén
  • person_outline Thomas Nordahl Petersen

Publication for MGmapper

MGmapper citations


Direct whole genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

Malar J
PMCID: 5824530
PMID: 29471822
DOI: 10.1186/s12936-018-2232-6

[…] to paired-end sequencing on the Illumina Miseq. Raw sequences were quality-trimmed and mapped to a variety of databases, including a human database and a custom-made malaria database (see “”), using MGmapper []. Table  lists the percentages of quality trimmed raw reads mapping to human, malaria and other databases. On average, the parasite content was 61% across the five samples, ranging however […]


Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

PMCID: 5793167
PMID: 29300319
DOI: 10.3390/genes9010014

[…] proach has been used in different classifiers, e.g., Kraken, published in 2014 [], CLARK (CLAssifier based on Reduced K-mers) published in 2015 [], Kaiju published in 2016 [], and metagenomic mapper (MGmapper) published in 2017 []. An example of a reference-based tool that only focuses on a defined set of strain-specific marker genes is the metagenomic phylogenetic analysis (MetaPhlAn) []. All the […]


Gene Based Pathogen Detection: Can We Use qPCR to Predict the Outcome of Diagnostic Metagenomics?

PMCID: 5704245
PMID: 29156625
DOI: 10.3390/genes8110332

[…] pported by the sample of 10 g (QIAamp 5c) spiked with 106 CFU/g C. jejuni, which was positive in both qPCR and Kraken, but with a quite low Kraken target ratio. Both 10-g samples were negative in the MGmapper analysis. The inhibition of Campylobacter detection in 10-g samples was contrary to the statistically significant increase in hits to Salmonella when increasing the sample size (QIAamp 5b and […]


Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

PMCID: 5707535
PMID: 29099783
DOI: 10.3390/v9110328

[…] bins predicted to be of non-phage origin are due to a limited diversity in the previously sequenced phage genomes rather than, e.g., contamination. This hypothesis is supported by the analysis using MGmapper, which showed that only a negligible amount of the raw sequence reads mapped to reference databases containing sequences from Bacteria, Archaea, MetaHitAssembly, HumanMicrobiome, Bacteria_dra […]


Evaluating next generation sequencing for direct clinical diagnostics in diarrhoeal disease

PMCID: 5495851
PMID: 28285331
DOI: 10.1007/s10096-017-2947-2
call_split See protocol

[…] dtA, cdtB, cdtC, ciaB, flaA, flaB, flaC), C. difficile (cdtA, cdtB, tcdA, tcdB), S. enterica (invA, invB, invE, invG, invH, invJ, sseA, sseB, sseC, sseD, sseE) and Y. enterocolitica (inv, ystA) using MGmapper (, mapping against the Virulence Factors Database ( [, ]. For the available isolates, the proportion of the genome sequence […]


Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing

PLoS One
PMCID: 5242460
PMID: 28099518
DOI: 10.1371/journal.pone.0170199

[…] The distribution of viral species was determined using MGmapper software version 2.2 ( []. The MGmapper tool follows three main steps: quality assessment of the raw reads, mapping of reads to the reference databas […]

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MGmapper institution(s)
Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark; National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
MGmapper funding source(s)
Supported by the European Community’s Seventh Framework Programme [FP7/2007–2013], under grant agreement n˚ 613754, and by The Villum Foundation (VKR023052).

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