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Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Author

Listed:
  • Ivan Sović

    (Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore
    Centre for Informatics and Computing, Ruđer Bošković Institute)

  • Mile Šikić

    (Faculty of Electrical Engineering and Computing, University of Zagreb
    Bioinformatics Institute)

  • Andreas Wilm

    (Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore)

  • Shannon Nicole Fenlon

    (Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore
    Faculty of Medicine and Institute for Life Sciences, University of Southampton)

  • Swaine Chen

    (Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore
    Yong Loo Lin School of Medicine, National University of Singapore)

  • Niranjan Nagarajan

    (Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore)

Abstract

Realizing the democratic promise of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. Here we present GraphMap, a mapping algorithm designed to analyse nanopore sequencing reads, which progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long reads with speed and high precision (>95%). Evaluation on MinION sequencing data sets against short- and long-read mappers indicates that GraphMap increases mapping sensitivity by 10–80% and maps >95% of bases. GraphMap alignments enabled single-nucleotide variant calling on the human genome with increased sensitivity (15%) over the next best mapper, precise detection of structural variants from length 100 bp to 4 kbp, and species and strain-specific identification of pathogens using MinION reads. GraphMap is available open source under the MIT license at https://github.com/isovic/graphmap .

Suggested Citation

  • Ivan Sović & Mile Šikić & Andreas Wilm & Shannon Nicole Fenlon & Swaine Chen & Niranjan Nagarajan, 2016. "Fast and sensitive mapping of nanopore sequencing reads with GraphMap," Nature Communications, Nature, vol. 7(1), pages 1-11, September.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11307
    DOI: 10.1038/ncomms11307
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    Cited by:

    1. Mohammed Alser & Julien Eudine & Onur Mutlu, 2025. "Taming large-scale genomic analyses via sparsified genomics," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
    2. Steve Hamner & Bonnie L. Brown & Nur A. Hasan & Michael J. Franklin & John Doyle & Margaret J. Eggers & Rita R. Colwell & Timothy E. Ford, 2019. "Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana," IJERPH, MDPI, vol. 16(7), pages 1-18, March.

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