University of Massachusetts Medical School Faculty Publications

UMMS Affiliation

Program in Molecular Medicine

Publication Date

2019-08-26

Document Type

Article Preprint

Disciplines

Computational Biology | Genomics

Abstract

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.

Keywords

Cactus, multiple genome alignment program, genomes, reference-free alignment

Rights and Permissions

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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.

DOI of Published Version

10.1101/730531

Source

bioRxiv 730531; doi: https://doi.org/10.1101/730531. Link to preprint on bioRxiv service.

Comments

Full author list omitted for brevity. For the full list of authors, see paper.

Journal/Book/Conference Title

bioRxiv

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

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