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An R interface to the GMAP/GSNAP/GSTRUCT suite

Bioconductor version: Release (3.19)

GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

Author: Cory Barr, Thomas Wu, Michael Lawrence

Maintainer: Michael Lawrence <michafla at>

Citation (from within R, enter citation("gmapR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

gmapR PDF R Script
Reference Manual PDF


biocViews Alignment, Software
Version 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (12 years)
License Artistic-2.0
Depends R (>= 2.15.0), methods, GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.31.8), Rsamtools(>= 1.31.2)
Imports S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), BiocGenerics(>= 0.25.1), rtracklayer(>= 1.39.7), GenomicFeatures(>= 1.31.3), Biostrings, VariantAnnotation(>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments(>= 1.15.6), BiocParallel
System Requirements
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Suggests RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3,, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
Linking To
Depends On Me HTSeqGenie
Imports Me
Suggests Me VariantTools, VariantToolsData
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package gmapR_1.46.0.tar.gz
Windows Binary
macOS Binary (x86_64) gmapR_1.46.0.tgz
macOS Binary (arm64) gmapR_1.46.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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