MGmapper protocols

View MGmapper computational protocol

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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 in pipeline

2017
PMCID: 5242460
PMID: 28099518
DOI: 10.1371/journal.pone.0170199

[…] runs with an average output of 1.4 × 106 250 bp paired-end reads per sample ()., 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 databases, and post-processing of mapping results. quality assessment […]


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MGmapper in publications

 (7)
PMCID: 5824530
PMID: 29471822
DOI: 10.1186/s12936-018-2232-6

[…] e. the pooled nexteraxt libraries were loaded onto an illumina miseq reagent cartridge using miseq reagent kit v3 and 500 cycles with a standard flow cell., paired end reads were analysed with mgmapper v. 2.0 [, ], available from the center for genomic epidemiology (cge). reads were trimmed from bases with a quality score below 30 (phred), and paired reads were mapped to the following […]

PMCID: 5707535
PMID: 29099783
DOI: 10.3390/v9110328

[…] resulting from trimming, were compensated using cmpfastq []., reads mapping to phix174 phage (nc_001422.1), which is used as an internal control in illumina sequencing, were removed by running mgmapper []. mgmapper is a pipeline that takes a fastq file as input and aligns reads to built-in databases using burrows-wheeler alignment algorithm (bwa) []. if none of the databases is specified […]

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

[…] hospital, denmark. ten samples from healthy individuals were also included. dna was extracted from faecal samples and sequenced on the illumina miseq system. species distribution was determined with mgmapper and ngs-based diagnostic prediction was performed based on the relative abundance of pathogenic bacteria and giardia and detection of pathogen-specific virulence genes. ngs-based diagnostic […]

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

[…] the 64 samples were sequenced on three illumina miseq runs with an average output of 1.4 × 106 250 bp paired-end reads per sample ()., 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 […]

PMCID: 5080404
PMID: 27822556
DOI: 10.1128/mSystems.00095-16

[…] xt dna library preparation guide for the miseq system part 15031942 rev. d, using paired-end v2 2 × 250-bp sequencing. the taxonomic microbiome compositions were determined through the use of the mgmapper pipeline (t. n. petersen, o. lukjancenko, m. c. f. thomsen, m. m. sperotto, o. lund, f. m. aarestrup, and t. sicheritz-pontén, unpublished data). for details regarding the metagenomics-based […]


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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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