Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.

ABSTRACT: Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with

SUBMITTER: Kajitani R 

PROVIDER: S-EPMC4120091 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature