TY  - JOUR
A1  - Kolmogorov, Mikhail
A1  - Armstrong, Joel
A1  - Raney, Brian J.
A1  - Streeter, Ian
A1  - Dunn, Matthew
A1  - Yang, Fengtang
A1  - Odom, Duncan
A1  - Flicek, Paul
A1  - Keane, Thomas M.
A1  - Thybert, David
A1  - Paten, Benedict
A1  - Pham, Son
T1  - Chromosome assembly of large and complex genomes using multiple references
Y1  - 2018/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1720 
EP  - 1732 
DO  - 10.1101/gr.236273.118 
VL  - 28 
IS  - 11 
UR  - http://genome.cshlp.org/content/28/11/1720.abstract 
N2  - 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. 
ER  -