title: Fast and accurate mapping of Complete Genomics reads.
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.
authors.affiliation: Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Donghyuk
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
authors.forename: Farhad
authors.initials: F
authors.lastname: Hormozdiari
authors.affiliation: Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
authors.forename: Hongyi
authors.initials: H
authors.lastname: Xin
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Faraz
authors.initials: F
authors.lastname: Hach
authors.affiliation: Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. Electronic address: onur@cmu.edu.
authors.forename: Onur
authors.initials: O
authors.lastname: Mutlu
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, Turkey. Electronic address: calkan@cs.bilkent.edu.tr.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
mesh_terms: D000465:Algorithms; D001330:Electronic Data Processing / Q000379:methods; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
keywords: Complete Genomics; Gapped reads; High throughput sequencing; Read mapping