Haoyu Cheng retweeted
Coding agents are helping scientists spend more time advancing research, taking on everything from routine maintenance and targeted optimization to complete redesigns and new systems.
While agents can reliably execute on ambitious projects, researchers must still define the scientific questions, verify results, and take a stance on long-term ownership.
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.
biorxiv.org/content/10.1101/…
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
biorxiv.org/content/10.1101/…
Haoyu Cheng retweeted
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.
Exciting news! The latest hifiasm release from @ChengChhy and @lh3lh3 adds beta support for @nanopore simplex R10 reads. Initial results look very promising. 🚀
Check it out: github.com/chhylp123/hifiasm…"
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! github.com/chhylp123/hifiasm…
My new lab at @YaleBIDS is looking for a couple of postdocs, students and RAs in bioinformatics, genomics, machine learning and related fields (postdocs.yale.edu/postdoctor…). Heartfelt thanks to my mentor @lh3lh3 and collaborators for their incredible support!
Haoyu Cheng retweeted
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 arxiv.org/abs/2409.00613
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 arxiv.org/abs/2306.03399
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: github.com/chhylp123/hifiasm…
Haoyu Cheng retweeted
Today is the big day! The #T2T consortium is claiming victory and announcing that we have finally uncovered every last bit of the human genome! The papers are out today 🥳🧬 science.org/toc/science/376/…
Haoyu Cheng retweeted
The previous hifiasm paper described haplotype-resolved assembly with trio data. In this new paper, @ChengChhy achieves chromosome-long phased assembly without parents. Tested for human and non-human species. A single executable and one command line for the entire process.
The latest hifiasm for single-sample haplotype-resolved assemblies from our lab @lh3lh3 is published on Nature Biotechnology @NatureBiotech. Journal paper: nature.com/articles/s41587-0… and read-only link: rdcu.be/cJM9E.
Haoyu Cheng retweeted
Latest from @ChengChhy, @lh3lh3 and collaborators:
Haplotype-resolved genome assemblies produced by the new #hifiasm algorithm could accurately reveal complex genetic variations in #cancer genomes. Further development may lead to high-quality cancer #genome assemblies.
The latest hifiasm for single-sample haplotype-resolved assemblies from our lab @lh3lh3 is published on Nature Biotechnology @NatureBiotech. Journal paper: nature.com/articles/s41587-0… and read-only link: rdcu.be/cJM9E.
We hope it will not only enable routine single-sample fully-phased assemblies, but also will be a better solution for complex SV calling.
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.
Haoyu Cheng retweeted
Yet another genome assembler, this time it is written in Rust.
Peregrine-2021: A faster and minimum genome assembler for long-reads with good enough accuracy
github.com/cschin/peregrine-…
#genomics #bioinformatics #rustlang
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 (arxiv.org/abs/2109.04785). We believe haplotype-resolved assembly for every diploid individual is becoming real before our eyes
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.
We also want to thank our collaborators @erichjarvis @ofedrigo @LaraUrban42 @ProfGemmell @ Klaus-Peter Koepfli for the fantastic help to improve and validate the results.