Format

Send to

Choose Destination
Methods. 2015 Jun;79-80:3-10. doi: 10.1016/j.ymeth.2014.10.012. Epub 2014 Oct 22.

Fast and accurate mapping of Complete Genomics reads.

Author information

1
Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
2
Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
3
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
4
Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. Electronic address: onur@cmu.edu.
5
Department of Computer Engineering, Bilkent University, Ankara, Turkey. Electronic address: calkan@cs.bilkent.edu.tr.

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

PMID:
25461772
PMCID:
PMC4406782
DOI:
10.1016/j.ymeth.2014.10.012
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Elsevier Science Icon for PubMed Central
Loading ...
Support Center