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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/10.110…

Miniprot-0.15 released with minor improvement to alignment around tandem gene duplications. github.com/lh3/miniprot/r…

Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/sho…

Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling biorxiv.org/content/10.110… #biorxiv_bioinfo

Excited to share that Ajay's paper is now out Nature Genetics : Transcriptome-wide analysis of differential expression in perturbation atlases rdcu.be/eiyI3

【Great update by hifiasm】T2T genome assembly using on ONT-only data(20k) - test by Benagen !!! Results 1： for simple genome, use only sequencing sample reads, using hifiasm (ont), directly reached the T2T level. Result 2 Compared with hifi assembly, ONT-only with hifiasm

If you want to check if a human gene has copy-number changes or lands in a complex region, try pangene.bioinweb.org. Recently updated with more and better assemblies.

【Great update by hifiasm Heng Li】 ONT-only get near T2T genome assembly - benagen test data v2! Only 50x ONT Oxford Nanopore data can get near T2T assembly, and 80x is suitable for haplotype assembly👏.

In this blog, Lakmal outlines Oxford Nanopore's roadmap to proteomics. nanoporetech.com/blog/london-ca… #nanoporeconf

Oxford Nanopore Tech Update LC2025. My full analysis of what this means for NGS and Multi-Omics, including the new Proteomics PoC. open.substack.com/pub/albertvile…

New metagenome assembler for @Nanopore R10 and PacBio HiFi reads from Jim Shaw

Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kmers…

This seems like an awesome course! jshun.csail.mit.edu/6506-s24/! If there were more hours in the day, I'd want to put something like this together at UMD.

Our lab is hiring! We are looking for a postdoc in the area of immunology/microbiology+ML, or in pure method/software development. More information about our lab at: mourisl.github.io

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment. arxiv.org/abs/2506.12986

FastGA: Fast Genome Alignment biorxiv.org/content/10.110… #biorxiv_bioinfo

Haplotype-aware long-read error correction biorxiv.org/content/10.110… #biorxiv_genomic

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

Detecting Foldback Artifacts in Long Reads biorxiv.org/content/10.110… #biorxiv_bioinfo

Excited to share our new preprint on detecting foldback artifacts in long reads with my advisors Matthew Meyerson and Heng Li! Stop by poster C-180 on Wednesday at ISMB/ECCB2025 to learn more and chat!