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Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, Joel (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
Hickey, Glenn (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
Diekhans, Mark (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
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Fiddes, Ian T. (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
Novak, Adam M. (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
Deran, Alden (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
Fang, Qi (författare)
BGI Shenzhen, Beishan Ind Zone, Shenzhen, Peoples R China.;Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Copenhagen, Denmark.
Xie, Duo (författare)
BGI Shenzhen, Beishan Ind Zone, Shenzhen, Peoples R China.;Univ Chinese Acad Sci, BGI Educ Ctr, Shenzhen, Peoples R China.
Feng, Shaohong (författare)
BGI Shenzhen, Beishan Ind Zone, Shenzhen, Peoples R China.;Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Yunnan, Peoples R China.
Stiller, Josefin (författare)
Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Copenhagen, Denmark.
Genereux, Diane (författare)
Broad Inst Harvard & Massachusetts Inst Technol M, Cambridge, MA USA.
Johnson, Jeremy (författare)
Broad Inst Harvard & Massachusetts Inst Technol M, Cambridge, MA USA.
Marinescu, Voichita Dana (författare)
Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinsk biokemi och mikrobiologi
Alföldi, Jessica (författare)
Broad Inst Harvard & Massachusetts Inst Technol M, Cambridge, MA USA.
Harris, Robert S. (författare)
Penn State Univ, Dept Biol, University Pk, PA 16802 USA.
Lindblad-Toh, Kerstin (författare)
Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Broad Inst Harvard & Massachusetts Inst Technol M, Cambridge, MA USA.
Haussler, David (författare)
Howard Hughes Med Inst, Chevy Chase, MD USA.
Karlsson, Elinor (författare)
Broad Inst Harvard & Massachusetts Inst Technol M, Cambridge, MA USA.;Univ Massachusetts, Sch Med, Program Mol Med, Worcester, MA USA.;Univ Massachusetts, Sch Med, Bioinformat & Integrat Biol, Worcester, MA USA.
Jarvis, Erich D. (författare)
Howard Hughes Med Inst, Chevy Chase, MD USA.;Rockefeller Univ, Lab Neurogenet Language, 1230 York Ave, New York, NY 10021 USA.
Zhang, Guojie (författare)
Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Copenhagen, Denmark.;Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming, Yunnan, Peoples R China.;Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China.;BGI Shenzhen, China Natl GeneBank, Shenzhen, Peoples R China.
Paten, Benedict (författare)
UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA.
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UC Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA BGI Shenzhen, Beishan Ind Zone, Shenzhen, Peoples R China.;Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Copenhagen, Denmark. (creator_code:org_t)
2020-11-11
2020
Engelska.
Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 587:7833, s. 246-251
Relaterad länk:
https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
https://www.nature.c...
https://urn.kb.se/re...
https://doi.org/10.1...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
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  • New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies(1-3). For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database(4) increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies(5) are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus(6), 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 sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far. The Progressive Cactus program can create reference-free alignments of hundreds of large vertebrate genomes efficiently, and is used for the alignment of more than 600 amniote genomes.

Ämnesord

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

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