RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Genome Biology

Sebastian Soyk¹  Sara Goodwin¹  Zachary B. Lippman¹  Xingang Wang¹  Srividya Ramakrishnan²  Michael Alonge²  Michael C. Schatz²  Fritz J. Sedlazeck³ 

[1] Cold Spring Harbor Laboratory;Department of Computer Science, Johns Hopkins University;Human Genome Sequencing Center, Baylor College of Medicine;

关键词: Pseudomolecule;    Reference-guided;    Genome assembly;    Scaffolding;    Genome alignment;    Long-read sequencing;   

DOI  :  10.1186/s13059-019-1829-6

来源: DOAJ

【 摘 要 】

Abstract We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO.

【 授权许可】

Unknown