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CompStor Novos: low cost yet fast assembly-based variant calling for personal genomes

Travis Oenning, Taejeong Bae, Aravind Iyengar, Barrett Brickner, Madushanka Soysa, Nicholas Wright, Prasanth Kumar, Suneel Indupuru, Alexej Abyzov, View ORCID ProfileJonathan Coker
doi: https://doi.org/10.1101/486092
Travis Oenning
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Taejeong Bae
2Mayo Clinic, Department of Health Sciences Research, Rochester, MN 55905
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Aravind Iyengar
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Barrett Brickner
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Madushanka Soysa
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Nicholas Wright
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Prasanth Kumar
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Suneel Indupuru
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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Alexej Abyzov
2Mayo Clinic, Department of Health Sciences Research, Rochester, MN 55905
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Jonathan Coker
1OmniTier, Inc., Rochester, MN 55901 and Milpitas, CA 95035
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  • ORCID record for Jonathan Coker
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Abstract

Application of assembly methods for personal genome analysis from next generation sequencing data has been limited by the requirement for an expensive supercomputer hardware or long computation times when using ordinary resources. We describe CompStor™ Novos, achieving supercomputer-class performance in de novo assembly computation time on standard server hardware, based on a tiered-memory implementation. Run on commercial off-the-shelf servers, Novos assembly is more precise and 10-20 times faster than that of existing assembly algorithms. Furthermore, we integrated Novos into a variant calling pipeline and demonstrate that both compute times and precision of calling point variants and indels compare well with standard alignment-based pipelines. Additionally, assembly eliminates bias in the estimation of allele frequency for indels and naturally enables discovery of breakpoints for structural variants with base pair resolution. Thus, Novos bridges the gap between alignment-based and assembly-based genome analyses. Extension and adaption of its underlying algorithm will help quickly and fully harvest information in sequencing reads for personal genome reconstruction.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted December 04, 2018.
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CompStor Novos: low cost yet fast assembly-based variant calling for personal genomes
Travis Oenning, Taejeong Bae, Aravind Iyengar, Barrett Brickner, Madushanka Soysa, Nicholas Wright, Prasanth Kumar, Suneel Indupuru, Alexej Abyzov, Jonathan Coker
bioRxiv 486092; doi: https://doi.org/10.1101/486092
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CompStor Novos: low cost yet fast assembly-based variant calling for personal genomes
Travis Oenning, Taejeong Bae, Aravind Iyengar, Barrett Brickner, Madushanka Soysa, Nicholas Wright, Prasanth Kumar, Suneel Indupuru, Alexej Abyzov, Jonathan Coker
bioRxiv 486092; doi: https://doi.org/10.1101/486092

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