PT  - JOURNAL ARTICLE
AU  - Ivan Sovic
AU  - Mile Sikic
AU  - Andreas Wilm
AU  - Shannon Nicole Fenlon
AU  - Swaine Chen
AU  - Niranjan Nagarajan
TI  - Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap
AID  - 10.1101/020719
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 020719
4099  - http://biorxiv.org/content/early/2015/06/10/020719.short
4100  - http://biorxiv.org/content/early/2015/06/10/020719.full
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.