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