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 Heng Li. Source code: github.com/chhylp123/hifi…

Releasing ClairS, a somatic variant caller for paired samples and ONT reads ⚙️github.com/HKU-BAL/Clairs. The figure shows the SNV performance at 70/45-fold SEQC2 HCC1395/BL of ONT R10.4.1 data. At AF≥0.20, 98.12% precision and 99.15% recall. AF≥0.05, 94.26% and 87.46%. 1/3

The recent announcement of Mojo by Modular has got me excited! It promises to be an ideal programming language for bioinformatics tool development. Jeremy Howard's post is a great intro to Mojo: fast.ai/posts/2023-05-… And my brief thoughts here: rrwick.github.io/2023/06/02/moj…

New preprint📢 miniBUSCO: a faster and more accurate reimplementation of BUSCO.⚡️Assess assembly completeness for a human genome within 30 minutes⏱️and achieve improved agreement with annotation completeness.🧬Thanks Dr. Li Heng Li biorxiv.org/content/10.110…

Excited to share our new t2t assembly algorithm for diploid and polyploid genomes! Using 132 assembled haplotypes from the Human Pangenome Reference Consortium , we show that our approach is cost-efficient, robust, and could achieve t2t assemblies without high coverage reads arxiv.org/abs/2306.03399

Delighted to share hifieval, our new method that evaluates haplotype-aware long read error correction (EC) tools. We hope the caveats of EC algorithms it reveals can help users to develop better EC tools, which would be essential to high-quality assembly. biorxiv.org/content/10.110…

Congrats to Heng Li, PhD (Heng Li), of Dana-Farber Data Science, selected for an @ISCB Fellowship and recognized for developing advanced bioinformatics algorithms and tools allowing DNA to be sequenced and analyzed in a fraction of the time it previously took. ms.spr.ly/6019gCG61

Richard Durbin and I have been working on a review titled "Genome assembly in the telomere-to-telomere era". We have put the preprint at arxiv.org/abs/2308.07877. Let us know if you have comments or suggestions. We would really appreciate!

ClairS is a somatic small variant caller for long-read, now in bioRxiv. Released in January and had rounds of updates, ClairS is getting stable and has been tested on ONT, HiFI, and Ilmn data. Here is the "Training data synthesis" figure and many more details in the manuscript.

BSAlign: a library for nucleotide sequence alignment biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Excited to announce the release of longcallR, our small variant caller for long-read RNA-seq data! Big thanks to Heng Li. Also, catch my talk at RECOMBseq this Sunday April 28th at 1:50 pm. Can't wait to see you there! Github: github.com/huangnengCSU/l…

Excited to share our latest research published in Nature Communications ! Check out our paper on [transposable element detection] here: nature.com/articles/s4146…. Dive into our code and data on GitHub: github.com/CSU-KangHu/HiTE.

The Floria paper is now out in Bioinformatics! Fast and accurate strain haplotyping in metagenomes by the amazing Jim Shaw & jsgounot. Check it out: github.com/bluenote-1577/… It was great to collaborate with Yun William Yu academic.oup.com/bioinformatics…

Now this is cool! What will generative genome AI teach us about us? nature.com/articles/s4225…

I'm happy to share the results of my rotation with Heng Li: biorxiv.org/content/10.110… We co-assembled reads from paired tumor-normal samples, then examined the structure of the co-assembly graph to identify large-scale somatic structural variation (focusing on translocations)

Excited to announce Splam is now published in Genome Biology! Splam, trained on thousands of splice junctions from GTEx, is your go-to tool for scoring splice junctions from alignment or annotation files. Mihaela Pertea Steven Salzberg 💙💛 Alan Mao doi.org/10.1186/s13059…

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/longc…

Exicted to share our recent work, longcallD, for long-read variant calling. More features are coming! Many thanks to my supervisor Dr. Heng Li Heng Li!!!