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Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Sović, Ivan; Šikić, Mile; Wilm, Andreas; Fenlon, Shannon Nicole; Chen, Swaine (2016) Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nature Communications, 7 . pp. 11307-1. ISSN 2041-1723

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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.

Item Type: Article
Uncontrolled Keywords: mapping ; alignment ; sequencing ; nanopore
Subjects: NATURAL SCIENCES > Biology
TECHNICAL SCIENCES > Computing
Divisions: Center for Informatics and Computing
Projects:
Project titleProject leaderProject codeProject type
Algoritmi za analizu slijeda genoma-AGESAMile ŠikićUIP-11-2013-7353HRZZ
Depositing User: Ivan Sović
Date Deposited: 23 Feb 2017 15:03
Last Modified: 23 Feb 2017 15:03
URI: http://fulir.irb.hr/id/eprint/3391
DOI: 10.1038/ncomms11307

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