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      • Department of Computer Engineering
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      Accelerating read mapping with FastHASH

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      Author
      Xin, H.
      Lee, D.
      Hormozdiari, F.
      Yedkar, S.
      Mutlu, O.
      Alkan C.
      Date
      2013
      Source Title
      BMC Genomics
      Print ISSN
      1471-2164
      Publisher
      BioMed Central Ltd.
      Volume
      14
      Pages
      1 - 13
      Language
      English
      Type
      Article
      Item Usage Stats
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      338
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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.
      Keywords
      Reference genome
      True location
      Hash table
      Dynamic programming algorithm
      Edit distance
      Permalink
      http://hdl.handle.net/11693/21174
      Published Version (Please cite this version)
      http://dx.doi.org/10.1186/1471-2164-14-S1-S13
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      • Department of Computer Engineering 1368
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