ConPADE: genome assembly ploidy estimation from next-generation sequencing data.

ABSTRACT: As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In

SUBMITTER: Margarido GR 

PROVIDER: S-EPMC4400156 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature