The MaSuRCA genome assembler.

ABSTRACT:

Motivation

Second-generation sequencing technologies produce high coverage of the genome by short reads at a low cost, which has prompted development of new assembly methods. In particular, multiple algorithms based on de Bruijn graphs have been shown to be effective for the assembly problem. In this article, we describe a new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error. Our method transforms large numbers of paired-end reads into a much smaller number of longer 'super-reads'. The use of super-reads allows us to assemble combinations of Illumina reads of differing lengths together with longer r

SUBMITTER: Zimin AV 

PROVIDER: S-EPMC3799473 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature