Unknown

Dataset Information

0

Chromosome assembly of large and complex genomes using multiple references.


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.

SUBMITTER: Kolmogorov M 

PROVIDER: S-EPMC6211643 | BioStudies | 2018-01-01

REPOSITORIES: biostudies

Similar Datasets

2015-01-01 | S-EPMC4542186 | BioStudies
2018-01-01 | S-EPMC5880236 | BioStudies
2017-01-01 | S-EPMC5411772 | BioStudies
2014-01-01 | S-EPMC4076250 | BioStudies
2020-01-01 | S-EPMC7247394 | BioStudies
2017-01-01 | S-EPMC5310280 | BioStudies
2013-01-01 | S-EPMC4053942 | BioStudies
1000-01-01 | S-EPMC3562798 | BioStudies
2015-01-01 | S-EPMC4348652 | BioStudies
2012-01-01 | S-EPMC3707490 | BioStudies