Gene

Biology

Reference genome

Scalability

Computer science

Sequence assembly

Computational biology

Evolutionary biology

Bacterial artificial chromosome

Genetics

Transcriptome

Database

Genome

Mutant

Genomics

Contig

Gene expression

Chromosome

Arabidopsis thaliana

Genome biology

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 .

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