RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
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ABSTRACT:
SUBMITTER: Alonge M
PROVIDER: S-EPMC6816165 | biostudies-literature | 2019 Oct
REPOSITORIES: biostudies-literature
Publications
RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Alonge Michael M Soyk Sebastian S Ramakrishnan Srividya S Wang Xingang X Goodwin Sara S Sedlazeck Fritz J FJ Lippman Zachary B ZB Schatz Michael C MC
Genome biology 20191028 1
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 RaGO ...[more]
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