Stefan Mileschin

Better than Minecraft

Boffins have emerged from their smoke filled labs with a new technique to reconstruct genomes on something as basic as a PC.

According to Phys.Org the technique is about a hundred times faster than current state-of-the-art approaches and uses one-fifth the resources.

The study, published September 14 in the journal Cell Systems, allows for a more compact representation of genome data inspired by the way in which words, rather than letters, offer condensed building blocks for language models.

To approach genome assembly more efficiently than current techniques, which involve making pairwise comparisons between all pairs of reads, [researchers] turned to language models.

Unfortunately the process involves returning to nightmare terminology of sixth form biology class which used to wake us up in the middle of the night with a cold sweat.

Basically the method builds on he concept of a de Bruijn graph, a simple, efficient data structure used for genome assembly, the researchers developed a minimiser-space de Bruin graph (mdBG), which uses short sequences of nucleotides called minimisers instead of single nucleotides.

https://fudzilla.com/news/53536-buil...ome-on-your-pc