Accelerating read mapping with FastHASH

Date
2013
Authors
Xin, H.
Lee, D.
Hormozdiari, F.
Yedkar, S.
Mutlu, O.
Alkan C.
Advisor
Supervisor
Co-Advisor
Co-Supervisor
Instructor
Source Title
BMC Genomics
Print ISSN
1471-2164
Electronic ISSN
Publisher
BioMed Central Ltd.
Volume
14
Issue
Pages
1 - 13
Language
English
Type
Article
Journal Title
Journal ISSN
Volume Title
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Abstract

With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS. We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection. We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness. © 2013 Xin et al.

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Book Title
Keywords
Reference genome, True location, Hash table, Dynamic programming algorithm, Edit distance
Citation
Published Version (Please cite this version)