RT Journal Article
SR Electronic
T1 MaGuS: a tool for map-guided scaffolding and quality assessment of genome assemblies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 032045
DO 10.1101/032045
A1 Mohammed-Amin Madoui
A1 Carole Dossat
A1 Léo d’Agata
A1 Jan van Oeveren
A1 Edwin van der Vossen
A1 Jean-Marc Aury
YR 2015
UL http://biorxiv.org/content/early/2015/11/17/032045.abstract
AB Background Scaffolding is a crucial step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in continuity 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 genome map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the continuity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase continuity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency.Conclusions MaGuS is a powerful reference-free evaluator of assembly quality and a map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the continuity of large and complex genome assemblies.