New preprint on hifiasm (ONT)! We can now achieve near T2T human genome assembly using only ONT Simplex reads—in just half a day, with or without ultra-long sequencing.
https://t.co/0tGqDGVn55
Telomere-to-telomere de novo assembly from standard ONT reads (LSK114, Simplex).
A really exciting advance—makes high-quality assembly practical for population-scale sequencing!
Preprint from @ChengChhy, @lh3lh3 and colleagues
https://t.co/VpQMC0DfLA
@XLR@lh3lh3@vellamike@nanopore The new version of hifiasm performs phasing, improved full-length base-level alignment rather than window-based alignment, and considers base quality.
The latest hifiasm can directly assemble standard @nanopore simplex R10 reads, without HERRO correction or other preprocessing, to phased contigs of contiguity comparable to HiFi assembly. Like before, you can further add ultra-long, Hi-C or trio data for better assembly.
Hifiasm 0.21.0 has been released. It now has a beta module for direct assembly of ONT R10 simplex reads. Initial tests with regular simplex reads show very promising results! https://t.co/4mmPylKusz
My new lab at @YaleBIDS is looking for a couple of postdocs, students and RAs in bioinformatics, genomics, machine learning and related fields (https://t.co/ZH5YZUfQ8R). Heartfelt thanks to my mentor @lh3lh3 and collaborators for their incredible support!
Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB https://t.co/DiRwZNHVVa
Excited to share our new t2t assembly algorithm for diploid and polyploid genomes! Using 132 assembled haplotypes from the @HumanPangenome , we show that our approach is cost-efficient, robust, and could achieve t2t assemblies without high coverage reads https://t.co/CCvKmsA2se
@basti_beier@HumanPangenome We actually used the UL reads >=50kb/100kb for the assembly. There are very small fraction of UL reads that could be longer than 500kb/1Mb.
New hifiasm with the ultra-long integration is released! We tested it with four diploid human samples and got many T2T chromosomes. Any feedback will be much-appreciated @lh3lh3. Source code: https://t.co/63ujHGwfmp
@subgenomes@lh3lh3@PacBio@nanopore It is compatible with the old bin files, but still would be better to rerun the whole workflow from the raw reads. We would also be interested in if it could work for the polyploid genome (although it might have some parameters to be tuned).