echemi logo
Product
  • Product
  • Supplier
  • Inquiry
    Home > Biochemistry News > Biotechnology News > Scientists can now assemble a complete genome on a personal computer in minutes

    Scientists can now assemble a complete genome on a personal computer in minutes

    • Last Update: 2021-10-01
    • Source: Internet
    • Author: User
    Search more information of high quality chemicals, good prices and reliable suppliers, visit www.echemi.com

    "We can quickly assemble entire genomes and metagenomics, including microbial genomes, on an ordinary laptop computer," said Bonnie Berger, a professor of mathematics at MIT's Computer Science and Artificial Intelligence Laboratory and the author of the study
    .


    "This ability is essential to assess changes in the gut microbiota related to diseases and bacterial infections (such as sepsis) so that we can treat them faster and save lives


    Since the Human Genome Project (Human Genome Project), the genome assembly project has made considerable progress
    .


    In 2003, the Human Genome Project completed the first complete assembly of the human genome at a cost of approximately US$2.


    In order to achieve genome assembly more efficiently than current technologies, Bonnie Berger and his colleagues turned to language models
    .


    Current technology requires pairwise comparisons of all possible reading combinations


    Berger said: "Our minimal space de Bruijn diagrams store only a small part of the total nucleotides while preserving the entire genome structure, making them orders of magnitude more efficient than the classic de Bruijn diagrams
    .


    "

    The researchers applied their method to collect real HiFi data of Drosophila melanogaster (almost perfect single-molecule reading accuracy) and human genome data provided by Pacific Biosciences (PacBio)
    .


    When Berger and his colleagues evaluated the resulting genomes, compared with other genome assemblers, mdbg-based software required 33 times less time and random access memory (RAM) computing hardware 8 times less


    Next, Berger and his colleagues used their method to build an index of 661,406 bacterial genomes, which is by far the largest of its kind
    .


    They found that this new technology can search for all antimicrobial resistance genes in 13 minutes, while it takes 7 hours to use standard sequence alignment


    Berger said: "We know that this method is effective, but we don't know that after further optimizing the code, it can scale so well on real data
    .


    "

    Rayan Chikhi, a researcher and team leader at the Pasteur Institute and one of the authors of the study, said: "The overall idea is feasible and does not require some usually expensive pre-processing steps, such as the mistakes made by most other genome assembly methods.
    Correction
    .


    "

    Berger added: "We can also process sequencing data
    with an error rate of up to 4% .


    " "As the price of long-read sequencers with different error rates drops rapidly, this capability opens the door to the democratization of sequencing data analysis


    Berger pointed out that although the method currently performs best when processing PacBio HiFi readings, the error rate is much lower than 1%, and it may soon be compatible with the ultra-long reading of Oxford nanopores.
    The current errors of Oxford nanopores The rate is 5-12%, but it may soon provide 4% reads
    .

    Berger said: "This can help field scientists build rapid genomic testing sites and go beyond PCR and marker arrays that might miss important differences between genomes
    .


    "

    This work was supported by the National Institutes of Health, ANR Inception, PRAIRIE and PANGAIA
    .

    Journal Reference :

    1. Barış Ekim, Bonnie Berger, Rayan Chikhi.
      Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer .
      Cell Systems , 2021; DOI: 10.
      1016/j.
      cels.
      2021.
      08.
      009

    This article is an English version of an article which is originally in the Chinese language on echemi.com and is provided for information purposes only. This website makes no representation or warranty of any kind, either expressed or implied, as to the accuracy, completeness ownership or reliability of the article or any translations thereof. If you have any concerns or complaints relating to the article, please send an email, providing a detailed description of the concern or complaint, to service@echemi.com. A staff member will contact you within 5 working days. Once verified, infringing content will be removed immediately.

    Contact Us

    The source of this page with content of products and services is from Internet, which doesn't represent ECHEMI's opinion. If you have any queries, please write to service@echemi.com. It will be replied within 5 days.

    Moreover, if you find any instances of plagiarism from the page, please send email to service@echemi.com with relevant evidence.