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GEM-Mapper specifications


Unique identifier OMICS_02589
Name GEM-Mapper
Alternative name GEnome Multitool mapper
Software type Package/Module, Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS
Programming languages C, Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 3
Stability Stable
Maintained Yes




No version available


  • person_outline Santiago Marco-Sola
  • person_outline Simon Heath
  • person_outline Paolo Ribeca
  • person_outline Alejandro Chacon

Additional information

Publications for GEnome Multitool mapper

GEM-Mapper citations


Innate Cell Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus Infected Cells: A Functional and RNA seq Study

Sci Rep
PMCID: 5684396
PMID: 29133947
DOI: 10.1038/s41598-017-15629-6

[…] RNA-seq reads were re-aligned with the GEMtools RNA-seq pipeline v1.7 (, which is based on the GEM mapper, using the improved version of the sea bass annotation (described above). The pipeline aligns the reads in a sample in three phases, mapping against the sea bass reference genome, against a […]


High throughput annotation of full length long noncoding RNAs with Capture Long Read Sequencing

Nat Genet
PMCID: 5709232
PMID: 29106417
DOI: 10.1038/ng.3988

[…] (i.e., determine the tissue of origin of each ROI), for each adapter its middle 26-nt was selected. Each of the 26-mers derived from the indexed adapters contained the hexamer barcode in the center. GEM mapper was employed to demultiplex samples. PacBio reads were compiled into a FASTA file (one file per species) and indexed by GEM. Mapping the middle 26-mer of indexed adapters to the PacBio read […]


Transcriptional mechanisms underlying life‐history responses to climate change in the three‐spined stickleback

Evol Appl
PMCID: 5511362
PMID: 28717391
DOI: 10.1111/eva.12487

[…] 3.48, HCS and followed by generation of FASTQ sequence files by CASAVA. RNA‐seq reads were aligned with the GEMtools RNA‐seq pipeline v1.7 (, which is based on the GEM mapper (Marco‐Sola, Sammeth, Guigo, & Ribeca, ). The mapping is exhaustive, which means that the mapper searches for all possible mappings up to a certain number of mismatches. The pipeline aligne […]


The non coding variant rs1800734 enhances DCLK3 expression through long range interaction and promotes colorectal cancer progression

Nat Commun
PMCID: 5316867
PMID: 28195176
DOI: 10.1038/ncomms14418

[…] s used to visualize the targeted RNA-seq data and detect bi-allelic differential expression. The SYSCOL RNA-seq cohort was mapped to the human reference genome sequence (GRCh37 autosomes+X+Y+M) using GEM mapper. The reads with mapping quality <150 were excluded for further analysis. The genes were annotated using Ensemble 75. The reads of the genes were counted by ‘HTSeq' framework and normalized […]


Expression quantitative trait loci for PI3K/AKT pathway

PMCID: 5228698
PMID: 28072738
DOI: 10.1097/MD.0000000000005817

[…] U P < 2.2 × 10−6).[] The RNAseq data with low mapping quality (MAPQ < 150) were excluded in the current study. Then, mRNA reads were mapped with an average of 48.9 million reads per sample using the GEM mapper.[] The expression of mRNA was quantified as the sum of all transcript reads per kilobase per million mapped reads per gene.[] All the expression data were normalized by probabilistic estima […]


Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems

Cell Rep
PMCID: 5889099
PMID: 27851971
DOI: 10.1016/j.celrep.2016.10.054

[…] ocol. DNA was then exposed to two rounds of sodium bisulfite treatment using the EpiTect Bisulfite kit (QIAGEN), and paired-end DNA sequencing was performed using the Illumina Hi-Seq 2000.We used the GEM mapper () with two modified versions each of the human (GRCh37) and viral reference genomes: one with all C’s changed to T’s and another with all G’s changed to A’s. Reads were fully converted in […]


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GEM-Mapper institution(s)
Centro Nacional de Analisis Genomico, Barcelona, Spain; The Pirbright Institute, Woking, UK ; Universitat Autònoma de Barcelona (UAB);
GEM-Mapper funding source(s)
Supported by grant CSD2007-00050 from the Ministerio de Educación y Ciencia (Spain) and grant 1R01MH090941-01 from the US National Institutes of Health/National Human Genome Research Institute and the European Union 7th Framework integrating project Revolutionary Approaches and Devices for Nucleic Acid Analysis (READNA, funded under grant agreement Health-F4-2008-201418) and the European Union 7th Framework project European Sequencing and Genotyping Infrastructure (ESGI, funded under grant agreement 262055).

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