Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
Faure, R.; Hilaire, B.; Flot, J.-F.; Lavenier, D.
Show abstract
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an as-sembler that operates directly on these sketches. MSR produces compact representations that (i) are alignable sequences--two sequences align if and only if their MSR sketches align--and (ii) are collision-resistant, so distinct sequences yield distinct sketches with high probability, retaining small differences between closely related strains. Alice reduces long reads to short MSR sketches, uses a classic short-read assembly method to assemble those sketches and decompresses the result to obtain the final assembly. This strategy addresses the longstanding challenge of producing a strain-resolved assembly for a low computational cost. On an Adineta vaga genome, a mock gut community comprising five conspecific strains, and two real metagenomes (human stool and soil), Alice is an order of magnitude faster than state-of-the-art HiFi assemblers while delivering assemblies of comparable quality and improving recovery of highly similar strains.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.