OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly.

ABSTRACT:

Background

Genome sequencing and assembly are essential for revealing the secrets of life hidden in genomes. Because of repeats in most genomes, current programs collate sequencing data into a set of assembled sequences, called contigs, instead of a complete genome. Toward completing a genome, optical mapping is powerful in rendering the relative order of contigs on the genome, which is called scaffolding. However, connecting the neighboring contigs with nucleotide sequences requires further efforts. Nagarajian et al. have recently proposed a software module, FINISH, to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, however, are not yet satisfying.

Results

To increase the accuracy of contig connections,

SUBMITTER: Chen YM 

PROVIDER: S-EPMC4029551 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature