AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.

ABSTRACT:

Motivation

De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species.

Results

Here we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bru

SUBMITTER: Bao E 

PROVIDER: S-EPMC4058956 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature