Submitted by ja607 on
Title | RaGOO: fast and accurate reference-guided scaffolding of draft genomes. |
Publication Type | Journal Article |
Year of Publication | 2019 |
Authors | Alonge, M, Soyk, S, Ramakrishnan, S, Wang, X, Goodwin, S, Sedlazeck, FJ, Lippman, ZB, Schatz, MC |
Journal | Genome Biol |
Volume | 20 |
Issue | 1 |
Pagination | 224 |
Date Published | 2019 Oct 28 |
ISSN | 1474-760X |
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 . |
DOI | 10.1186/s13059-019-1829-6 |
Alternate Journal | Genome Biol. |
PubMed ID | 31661016 |
PubMed Central ID | PMC6816165 |
Grant List | DBI-1350041 / / National Science Foundation / IOS-1445025 / / National Science Foundation / IOS-1732253 / / National Science Foundation / IOS-1732253 / / National Science Foundation / MCB180087 / / National Science Foundation / R01-HG006677 / NH / NIH HHS / United States UM1 HG008898 / NH / NIH HHS / United States |