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Genome Res. 2018 Nov;28(11):1720-1732. doi: 10.1101/gr.236273.118. Epub 2018 Oct 19.

Chromosome assembly of large and complex genomes using multiple references.

Author information

1
Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.
2
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA.
3
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
4
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom.
5
Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, United Kingdom.
6
School of Life Sciences, University of Nottingham, Nottingham NG7 2NR, United Kingdom.
7
Earlham Institute, Norwich Research Park, Norwich NR4 7UG, United Kingdom.
8
BioTuring Incorporated, San Diego, California 92121, USA.

Abstract

Despite the rapid development of sequencing technologies, the assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in bioinformatics. To help address this difficulty, we developed Ragout 2, a reference-assisted assembly tool that works for large and complex genomes. By taking one or more target assemblies (generated from an NGS assembler) and one or multiple related reference genomes, Ragout 2 infers the evolutionary relationships between the genomes and builds the final assemblies using a genome rearrangement approach. By using Ragout 2, we transformed NGS assemblies of 16 laboratory mouse strains into sets of complete chromosomes, leaving <5% of sequence unlocalized per set. Various benchmarks, including PCR testing and realigning of long Pacific Biosciences (PacBio) reads, suggest only a small number of structural errors in the final assemblies, comparable with direct assembly approaches. We applied Ragout 2 to the Mus caroli and Mus pahari genomes, which exhibit karyotype-scale variations compared with other genomes from the Muridae family. Chromosome painting maps confirmed most large-scale rearrangements that Ragout 2 detected. We applied Ragout 2 to improve draft sequences of three ape genomes that have recently been published. Ragout 2 transformed three sets of contigs (generated using PacBio reads only) into chromosome-scale assemblies with accuracy comparable to chromosome assemblies generated in the original study using BioNano maps, Hi-C, BAC clones, and FISH.

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