Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era [preprint]
UMass Chan Affiliations
Program in Molecular MedicineDocument Type
PreprintPublication Date
2019-08-26Keywords
Cactusmultiple genome alignment program
genomes
reference-free alignment
Computational Biology
Genomics
Metadata
Show full item recordAbstract
Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.Source
bioRxiv 730531; doi: https://doi.org/10.1101/730531. Link to preprint on bioRxiv service.
DOI
10.1101/730531Permanent Link to this Item
http://hdl.handle.net/20.500.14038/29393Notes
Full author list omitted for brevity. For the full list of authors, see paper.
Rights
The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.Distribution License
http://creativecommons.org/licenses/by-nc-nd/4.0/ae974a485f413a2113503eed53cd6c53
10.1101/730531
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Except where otherwise noted, this item's license is described as The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
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