RT Journal Article
SR Electronic
T1 Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 020719
DO 10.1101/020719
A1 Ivan Sovic
A1 Mile Sikic
A1 Andreas Wilm
A1 Shannon Nicole Fenlon
A1 Swaine Chen
A1 Niranjan Nagarajan
YR 2015
UL http://biorxiv.org/content/early/2015/06/10/020719.abstract
AB Exploiting the power of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision (>95%). Evaluation on MinION sequencing datasets against short and long-read mappers indicates that GraphMap increases mapping sensitivity by at least 15-80%. GraphMap alignments are the first to demonstrate consensus calling with <1 error in 100,000 bases, variant calling on the human genome with 76% improvement in sensitivity over the next best mapper (BWA-MEM), precise detection of structural variants from 100bp to 4kbp in length 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.