A common PC is enough to assemble entire genomes in a few minutes, whether they are viruses, flies or human beings: to make this 'sprint' in research possible is a new technique that is a hundred times faster than the current ones despite exploiting only a fifth of the IT resources.
This is demonstrated by a study published in the journal Cell Systems by researchers from the Massachusetts Institute of Technology (MIT) in collaboration with the Pasteaur Institute in Paris.
The new technique owes its efficiency to the ability to give a more compact representation of the genome, not for single 'letters' (nucleotides) but for short 'words' (sequences of nucleotides). In addition to accelerating research, it can improve diagnostics and help save lives. The ability to rapidly reconstruct entire genomes may prove to be crucial, for example, "to verify changes in the intestinal microbiome linked to diseases and bacterial infections such as sepsis, which allows patients to be treated promptly", explains Bonnie Berger, mathematician at MIT.
The method was put to the test to assemble data related to the fruit fly and the human genome: the software took a thirty-third time and an eighth the time of Ram compared to other techniques currently available. The method was then used to create the index of a collection of over 600,000 bacterial genomes, the largest of its kind: the software allowed to go through the entire collection to identify antibiotic resistance genes in just 13 minutes. instead of seven hours.