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MGmapper specifications

Information


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

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Documentation


Maintainers


  • person_outline Thomas Sicheritz Pontén
  • person_outline Thomas Nordahl Petersen

Publication for MGmapper

MGmapper citations

 (10)
library_books

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

2018
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 […]

library_books

Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples

2018
Genes
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 […]

library_books

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

2017
Genes
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 […]

library_books

Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014

2017
Viruses
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 […]

call_split

Evaluating next generation sequencing for direct clinical diagnostics in diarrhoeal disease

2017
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 (https://cge.cbs.dtu.dk/services/MGmapper), mapping against the Virulence Factors Database (http://www.mgc.ac.cn/VFs/) [, ]. For the available isolates, the proportion of the genome sequence […]

library_books

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

2017
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 (https://cge.cbs.dtu.dk/services/MGmapper/) []. 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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