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      • Department of Computer Engineering
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      Fast and accurate mapping of complete genomics reads

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      Author(s)
      Lee, D.
      Hormozdiari, F.
      Xin, H.
      Hach, F.
      Mutlu, O.
      Alkan C.
      Date
      2015
      Source Title
      Methods
      Print ISSN
      1046-2023
      Publisher
      Academic Press
      Volume
      79-80
      Pages
      3 - 10
      Language
      English
      Type
      Article
      Item Usage Stats
      154
      views
      119
      downloads
      Abstract
      Many recent advances in genomics and the expectations of personalized medicine are made possible thanks to power of high throughput sequencing (HTS) in sequencing large collections of human genomes. There are tens of different sequencing technologies currently available, and each HTS platform have different strengths and biases. This diversity both makes it possible to use different technologies to correct for shortcomings; but also requires to develop different algorithms for each platform due to the differences in data types and error models. The first problem to tackle in analyzing HTS data for resequencing applications is the read mapping stage, where many tools have been developed for the most popular HTS methods, but publicly available and open source aligners are still lacking for the Complete Genomics (CG) platform. Unfortunately, Burrows-Wheeler based methods are not practical for CG data due to the gapped nature of the reads generated by this method. Here we provide a sensitive read mapper (sirFAST) for the CG technology based on the seed-and-extend paradigm that can quickly map CG reads to a reference genome. We evaluate the performance and accuracy of sirFAST using both simulated and publicly available real data sets, showing high precision and recall rates.
      Keywords
      Complete genomics
      Gapped reads
      High throughput sequencing
      Read mapping
      DNA
      Accuracy
      Controlled study
      Data analysis software
      DNA sequence
      Gene mapping
      Genetic algorithm
      Genomics
      High throughput sequencing
      Human
      Human genome
      Indel mutation
      Personalized medicine
      Priority journal
      Sensitivity and specificity
      Permalink
      http://hdl.handle.net/11693/22814
      Published Version (Please cite this version)
      http://dx.doi.org/10.1016/j.ymeth.2014.10.012
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