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 | ||||||||
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| Uncontrolled Keywords: | mapping ; alignment ; sequencing ; nanopore | ||||||||
| Subjects: | NATURAL SCIENCES > Biology TECHNICAL SCIENCES > Computing |
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| Divisions: | Center for Informatics and Computing | ||||||||
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| Depositing User: | Ivan Sović | ||||||||
| Date Deposited: | 23 Feb 2017 15:03 | ||||||||
| URI: | http://fulir.irb.hr/id/eprint/3391 | ||||||||
| DOI: | 10.1038/ncomms11307 |
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