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

By Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J. Sedlazeck, Z. Lippman, Michael C. Schatz. Genome Biology, 2019

586 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/e496acee0bf81b502583afa26c5addc870db68af

Citations in the corpus

• Major impacts of widespread structural variation on gene expression and crop improvement in tomato (2020, unknown): “8924 were not sequenced in-house for this study, but rather come from a previous publication (Alonge et al., 2019).”
• Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, unknown): “M82 Illumina short-reads [17] were aligned to the draft Flye ONT assembly with BWA-MEM (v0.”
• Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, unknown): “The function h() maps contig terminus pairs to Hi-C scores (see Methods). d, nX plots showing the minimum sequence length (y-axis, log scale) needed to constitute a particular percentage of the assembly (x-axis). e, Ideogram showing contig boundaries (alternating color and gray) within the final sca”