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This picture shows a partial genome map of 661,405 bacterial genomes, each component representing the common structure of multiple genomes from closely related species
.
Scientists at the Massachusetts Institute of Technology (MIT) and the Pasteur Institute in France have developed a technology to reconstruct the entire genome (including the human genome) on a personal computer
.
This technique is a hundred times faster than the current state-of-the-art method and uses one-fifth of the resources
"We can quickly assemble entire genomes and metagenomics, including microbial genomes, on an ordinary laptop," said Bonnie Berger, Professor of Mathematics at the MIT Computer Science and Artificial Intelligence Laboratory and author of the study.
Berger) said
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, costing approximately US$2.
In order to achieve genome assembly more efficiently than current technologies, 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), as well as human genome data provided by PacBio
.
When Berger and his colleagues evaluated the resulting genomes, compared with other genome assemblers, mdBG-based software required 33 times less time and 8 times less random access memory (RAM) computing hardware
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 genes in 13 minutes, while it takes 7 hours to use standard sequence alignment
Berger said: "We know that our representation 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 those done by most other genome assembly methods.
Error correction
.
"
Berger added: “We can also process sequencing data
with an error rate of up to 4% .
With the rapid decline in the price of long-read sequencers with different error rates, 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, with an error rate far below 1%, it may soon be compatible with the ultra-long readings of Oxford Nanopores.
The current errors of Oxford Nanopores The rate is 5-12%, but it may soon provide 4% reads
.
Berger said: "We envision reaching out to field scientists to help them establish rapid genome testing sites, beyond PCR and marker arrays that might miss important differences between genomes
.
"
###
"Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer" https:// DOI: 10.
1016 /j.
cels.
2021.
08.
009
