A de novo genome assembly algorithm for repeats and nonrepeats.

ABSTRACT:

Background

Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses. Up to now, the performances of assembling repeats of these current assemblers are very poor.

Results

To improve this problem, we proposed a new genome assembly algorithm, named SWA, which has four properties: (1) assembling repeats and nonrepeats; (2) adopting a new overlapping extension strategy to extend each seed; (3) adopting sliding window to filter out the sequencing bias; and (4) proposing a compensational mechanism for low coverage datasets. SWA was evaluated and validated in both simulations and real sequencing datasets. The accuracy of

SUBMITTER: Lian S 

PROVIDER: S-EPMC4055594 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature