2018
DOI: 10.1101/gr.236273.118
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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 bu… Show more

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Cited by 100 publications
(71 citation statements)
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“…We first assembled the R. melanosticta scaffolds to chromosomes using the software Chromosomer [40]. This method generates draft chromosome level assemblies based on a BLAST alignment [61] between the reference genome and target genome scaffolds [39]. The algorithm considers a scaffold to be anchored to a specific position on the reference genome if the ratio between the first and second highest alignment score is higher than a predefined ratio threshold (default is 1.2).…”
Section: Single Reference Assisted Chromosome Level Assemblymentioning
confidence: 99%
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“…We first assembled the R. melanosticta scaffolds to chromosomes using the software Chromosomer [40]. This method generates draft chromosome level assemblies based on a BLAST alignment [61] between the reference genome and target genome scaffolds [39]. The algorithm considers a scaffold to be anchored to a specific position on the reference genome if the ratio between the first and second highest alignment score is higher than a predefined ratio threshold (default is 1.2).…”
Section: Single Reference Assisted Chromosome Level Assemblymentioning
confidence: 99%
“…The consistency of sequence adjacency across multiple genomes adds powerful information to referenced-based chromosome assembly [39,41]. We used the software Ragout 2 [39] to assemble the R. melanosticta scaffolds into chromosomes. Ragout uses phylogenetic information to reconstruct the most likely chromosome rearrangements for the target genome [39].…”
Section: Multiple Reference Assisted Chromosome Level Assemblymentioning
confidence: 99%
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