Joint work with @lh3lh3, @peter_j_park, and the ONT team @vellamike.

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.

RT @lh3lh3: The latest hifiasm can directly assemble standard @nanopore simplex R10 reads, without HERRO correction or other preprocessing,….

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!

My new lab at @YaleBIDS is looking for a couple of postdocs, students and RAs in bioinformatics, genomics, machine learning and related fields (. Heartfelt thanks to my mentor @lh3lh3 and collaborators for their incredible support!.

RT @lh3lh3: Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SM….

Many thanks to those who made this work possible! @asri_mobin Julian Lucas @sergekoren @lh3lh3.

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

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:

RT @aphillippy: Today is the big day! The #T2T consortium is claiming victory and announcing that we have finally uncovered every last bit….

RT @lh3lh3: The previous hifiasm paper described haplotype-resolved assembly with trio data. In this new paper, @ChengChhy achieves chromos….

RT @dfcidatascience: Latest from @ChengChhy, @lh3lh3 and collaborators: .Haplotype-resolved genome assemblies produced by the new #hifiasm….

We also want to thank our collaborators @erichjarvis @ofedrigo @LaraUrban42 @ProfGemmell @ Klaus-Peter Koepfli for the fantastic help, and the datasets from @darwintreelife and @genomeark.

We hope it will not only enable routine single-sample fully-phased assemblies, but also will be a better solution for complex SV calling.

The latest hifiasm for single-sample haplotype-resolved assemblies from our lab @lh3lh3 is published on Nature Biotechnology @NatureBiotech. Journal paper: and read-only link:

RT @infoecho: Yet another genome assembler, this time it is written in Rust. Peregrine-2021: A faster and minimum genome assembler for lon….

We also want to thank our collaborators @erichjarvis @ofedrigo @LaraUrban42 @ProfGemmell @ Klaus-Peter Koepfli for the fantastic help to improve and validate the results.

Only with HiFi reads, hifiasm also supports to output two highly contiguous primary assemblies, called dual assembly. We demonstrated dual assembly is more powerful than mapping-based methods in complex regions like GTF2IRD2. Assembly might be the ultimate solution to SV calling.

Our lab @lh3lh3 develops a single-sample phased assembler combining @PacBio HiFi and Hi-C, which has been heavily tested for human and non-human samples (. We believe haplotype-resolved assembly for every diploid individual is becoming real before our eyes.

RT @lh3lh3: Hifiasm published in @naturemethods. Preprint: Source code: Assemblies: https:….