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Statistical Genomics pp 283–334Cite as

GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1418))

Abstract

The programs GMAP and GSNAP, for aligning RNA-Seq and DNA-Seq datasets to genomes, have evolved along with advances in biological methodology to handle longer reads, larger volumes of data, and new types of biological assays. The genomic representation has been improved to include linear genomes that can compare sequences using single-instruction multiple-data (SIMD) instructions, compressed genomic hash tables with fast access using SIMD instructions, handling of large genomes with more than four billion bp, and enhanced suffix arrays (ESAs) with novel data structures for fast access. Improvements to the algorithms have included a greedy match-and-extend algorithm using suffix arrays, segment chaining using genomic hash tables, diagonalization using segmental hash tables, and nucleotide-level dynamic programming procedures that use SIMD instructions and eliminate the need for F-loop calculations. Enhancements to the functionality of the programs include standardization of indel positions, handling of ambiguous splicing, clipping and merging of overlapping paired-end reads, and alignments to circular chromosomes and alternate scaffolds. The programs have been adapted for use in pipelines by integrating their usage into R/Bioconductor packages such as gmapR and HTSeqGenie, and these pipelines have facilitated the discovery of numerous biological phenomena.

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Author information

Authors and Affiliations

  1. Genentech, South San Francisco, CA, USA

    Thomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker & Matthew J. Brauer

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  1. Thomas D. Wu
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  2. Jens Reeder
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  3. Michael Lawrence
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  4. Gabe Becker
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  5. Matthew J. Brauer
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Editors and Affiliations

  1. Ohio State University, Biomed Informatics, College of Medicine, Columbus, Ohio, USA

    Ewy Mathé

  2. National Cancer Institute, National Institutes of Health, Columbia, Maryland, USA

    Sean Davis

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Wu, T.D., Reeder, J., Lawrence, M., Becker, G., Brauer, M.J. (2016). GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality. In: Mathé, E., Davis, S. (eds) Statistical Genomics. Methods in Molecular Biology, vol 1418. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3578-9_15

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  • DOI: https://doi.org/10.1007/978-1-4939-3578-9_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3576-5

  • Online ISBN: 978-1-4939-3578-9

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