MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data.

ABSTRACT:

Background

Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring.

Results

We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding p

SUBMITTER: Madoui MA 

PROVIDER: S-EPMC4776351 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature