Bioconductor/R package gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite. 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.

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  1. Akalin, Altuna: Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen (2021)