Naslov
Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Autori
Sović, Ivan ; Šikić, Mile ; Wilm Andreas ; Fenlon, Shannon Nicole ; Chen, Swaine

Izvornik
Nature Communications (2041-1723) 7 (2016); 11307-1

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
mapping ; alignment ; sequencing ; nanopore

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo

POVEZANOST RADA