title: Fast and sensitive mapping of nanopore sequencing reads with GraphMap.
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.
authors.affiliation: Computational &Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore.|Centre for Informatics and Computing, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
authors.forename: Ivan
authors.initials: I
authors.lastname: Sović
authors.affiliation: Faculty of Electrical Engineering and Computing, Department of Electronic Systems and Information Processing, University of Zagreb, Unska 3, 10000 Zagreb, Croatia.|Bioinformatics Institute, Singapore 138671, Singapore.
authors.forename: Mile
authors.identifier: http://orcid.org/0000-0002-8370-0891
authors.initials: M
authors.lastname: Šikić
authors.affiliation: Computational &Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilm
authors.affiliation: 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, Southampton SO16 6YD, UK.
authors.forename: Shannon Nicole
authors.initials: SN
authors.lastname: Fenlon
authors.affiliation: Computational &Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore.|Division of Infectious Diseases, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore.
authors.forename: Swaine
authors.identifier: http://orcid.org/0000-0002-0107-2861
authors.initials: S
authors.lastname: Chen
authors.affiliation: Computational &Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore.
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D058608:Nanopores; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods