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Human Genome Assembly in 100 Minutes

View ORCID ProfileChen-Shan Chin, Asif Khalak
doi: https://doi.org/10.1101/705616
Chen-Shan Chin
Foundation for Biological Data Science
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  • For correspondence: chenshan@biologicaldatascience.org
Asif Khalak
Foundation for Biological Data Science
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Abstract

De novo genome assembly provides comprehensive, unbiased genomic information and makes it possible to gain insight into new DNA sequences not present in reference genomes. Many de novo human genomes have been published in the last few years, leveraging a combination of inexpensive short-read and single-molecule long-read technologies. As long-read DNA sequencers become more prevalent, the computational burden of generating assemblies persists as a critical factor. The most common approach to long-read assembly, using an overlap-layout-consensus (OLC) paradigm, requires all-to-all read comparisons, which quadratically scales in computational complexity with the number of reads. We assert that recently achievements in sequencing technology (i.e. with accuracy ~99% and read length ~10-15k) enables a fundamentally better strategy for OLC that is effectively linear rather than quadratic. Our genome assembly implementation, Peregrine uses sparse hierarchical minimizers (SHIMMER) to index reads thereby avoiding the need for an all-to-all read comparison step. Peregrine can assemble 30x human PacBio CCS read datasets in less than 30 CPU hours and around 100 wall-clock minutes to a high contiguity assembly (N50 > 20Mb). The continued advance of sequencing technologies coupled with the Peregrine assembler enables routine generation of human de novo assemblies. This will allow for population scale measurements of more comprehensive genomic variations -- beyond SNPs and small indels -- as well as novel applications requiring rapid access to de novo assemblies.

Footnotes

  • chenshan{at}biologicaldatascience.org

  • asif{at}biologicaldatascience.org

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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-NC 4.0 International license.
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Posted July 17, 2019.
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Human Genome Assembly in 100 Minutes
Chen-Shan Chin, Asif Khalak
bioRxiv 705616; doi: https://doi.org/10.1101/705616
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Human Genome Assembly in 100 Minutes
Chen-Shan Chin, Asif Khalak
bioRxiv 705616; doi: https://doi.org/10.1101/705616

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