Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Joel C. Armstrong; Glenn Hickey; Mark Diekhans; Alden Deran; Qi Fang; Duo Xie; Shaohong Feng; Josefin Stiller; Diane P. Genereux; Jeremy Johnson; Voichita Dana Marinescu; David H. Haussler; Jessica Alföldi; Kerstin Lindblad‐Toh; Elinor K. Karlsson; Erich David Jarvis; Guojie Zhang; Benedict Paten

doi:10.1101/730531

GenomicsbioRxivOct 15, 2019

Preprint

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

Joel C. Armstrong iD, Glenn Hickey iD, Mark Diekhans iD, Alden Deran, Qi Fang iD, Duo Xie iD, Shaohong Feng iD, Josefin Stiller iD, Diane P. Genereux iD, Jeremy Johnson iD, Voichita Dana Marinescu iD, David H. Haussler iD, Jessica Alföldi iD, Kerstin Lindblad‐Toh iD, Elinor K. Karlsson iD, Erich David Jarvis iD, Guojie Zhang iD, Benedict Paten iD

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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.