GEM-Mapper statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

GEM-Mapper specifications

Information


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

Download


download.png
github.png

Versioning


No version available

Maintainers


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

Additional information


https://sourceforge.net/projects/gemlibrary/files/?source=navbar

Publications for GEnome Multitool mapper

GEM-Mapper citations

 (13)
library_books

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

2017
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 (http://gemtools.github.io), 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 […]

library_books

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

2017
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 […]

library_books

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

2017
Evol Appl
PMCID: 5511362
PMID: 28717391
DOI: 10.1111/eva.12487

[…] 3.48, HCS 1.5.15.1) and followed by generation of FASTQ sequence files by CASAVA. RNA‐seq reads were aligned with the GEMtools RNA‐seq pipeline v1.7 (http://gemtools.github.io), 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 […]

library_books

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

2017
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 […]

library_books

Expression quantitative trait loci for PI3K/AKT pathway

2017
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 […]

library_books

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

2016
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 […]

Citations

Looking to check out a full list of citations?

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).

GEM-Mapper reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GEM-Mapper