Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Ivan Sović, Mile Šikić, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen and Niranjan Nagarajan ()
Additional contact information
Ivan Sović: Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore
Mile Šikić: Faculty of Electrical Engineering and Computing, University of Zagreb
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
Swaine Chen: Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore
Niranjan Nagarajan: Computational & Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore

Nature Communications, 2016, vol. 7, issue 1, 1-11

Abstract: 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 .

Date: 2016
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/ncomms11307 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11307

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms11307

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().