Introns have to come from somewhere, right? @celineh2ooo.bsky.social and I looked at multiple genome alignments with 1000s of genomes and found 342 cases where humans (and our relatives) had gained a new intron. Still not sure where these come from, but it's a fascinating question

Neng Huang developed longcallR for joint SNP calling and phasing from long RNA-seq reads, AND for identifying allele-specific splicing/junctions (ASJ). Although ASJs of statistical significance are rare, a large fraction involve unannotated junctions. In Rust!

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Excited to share a new update to Mumemto, scaling MUM and conserved element finding to any size pangenome! Preprint out now w/ @benlangmead.bsky.social. Mumemto scales to the new HPRC v2 release and beyond, and can merge in future assemblies without any recomputation! 1/n

Centrifuger has updated the pre-built index list to include this exciting GTDB new release r226 for taxonomic classification of sequencing data: github.com/mourisl/cent.... There is also a gtdb+refseq human/virus/fungi/contaminants index, hopefully will be useful for human microbiome studies.

Great 🧵 by Pierre on the Kaminari paper! In short, Kaminari is a simple and elegant, but highly effective index for approximate colored k-mer queries. The simplicity leads to very fast query, but with accuracy consistent with (or exceeding) best-in-class solutions; a very fun collaboration indeed!

Bioinformatics folks: check out our @biorxivpreprint on a new, very efficient and accurate system for automated genome annotation, EviAnn, led by my colleague Aleksey Zimin: www.biorxiv.org/content/10.1...

Check out our latest collaboration with UniProt, who has integrated over 700,000 experimentally validated epitopes to enhance its protein entries with detailed immune response information. This data is accessible via the UniProt Feature Viewer and API! 💻🔬🧪 #collaboration #immunology #proteins

The deadline for WABI 2025 has been extended (but is still rapidly approaching) wabiconf.github.io/2025/ * abstract deadline: May 12 (AoE) * paper deadline: May 15 (AoE) Consider submitting your exciting algorithmic bioinformatics work to the WABI conference!

Forgot to dustmasker the genomes before creating a Centrifuger index and indeed saw some misclassifications. Took a while to figure out and lessons learned... Need to implement a built-in masking step like Kraken2 in case forget doing it in the future..

Parsing GTF and FASTA files using the eccLib Library www.biorxiv.org/content/10.1... 🧬🖥️🧪 gitlab.platinum.edu.pl/eccdna/eccLib

Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs github.com/arcInstitute...

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

The Department of Human Genetics at the University of Utah is sponsoring the Rising Stars in Genetics and Genomics symposium! - We are seeking nominations bu June 1. - September 18-19, 2025 - Please share with the star postdocs that you know. docs.google.com/forms/d/e/1F...

The sequence analysis session of #RECOMB2025 is off to a great start with @jimshaw.bsky.social presenting devider, a new algorithm for haplotyping small sequences from long-read sequencing. www.biorxiv.org/content/10.1...

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.

Time to build a new index!!

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

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

minimap2 adds support for short read spliced RNA-seq alignment! lh3.github.io/2025/04/18/s...

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

fqgrep release 1.1.0 now speeds up searching FASTQ files! Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration. See more: github.com/fulcrumgenom...

Just published simd-sketch, a crate for fast bucket sketches. It's 7x to 30x faster than BinDash, by using the simd-minimizers crate for fast hashing, and a nearly branch-free implementation. Here's a blogpost with a survey of minhash history & methods, and evals: curiouscoding.nl/posts/simd-s...

Disease diagnostics using machine learning of B cell and T cell receptor sequences www.science.org/doi/10.1126/... TL;DR: BCRs ARE ALL YOU NEED! (Well actually .... keep reading) 1/

We just released a new version of piscem (should hit bioconda soon & a new version of simpleaf is imminent). The biggest improvement in this new version is increased mapping speed for scATAC-seq data, with the new version being 30-50% faster than the last release! github.com/COMBINE-lab/...

My PhD adviser Liliana Florea has developed a Coursera course "Bioinformatics Methods for Transcrptomics". A great resource to learn cutting-edge short- and long-read RNA-seq data analysis techniques: www.coursera.org/learn/bioinf...

We may have cut our last Canu release in 2024, but we are starting off 2025 with Verkko2! 🎉 Not only is it 4x faster than Verkko1, this version integrates Hi-C data for both phasing and scaffolding, enabling the automated assembly of acrocentric chromosomes! Preprint: www.biorxiv.org/content/10.1...

Wrapping up this year's work with a new release of Centrifuger: github.com/mourisl/cent... ! Finally implemented the abundance estimation module. I also found issues in Centrifuge's quantification procedure, so I add a script that uses "centrifuger-quant" to requantify Centrifuge's output.

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling www.biorxiv.org/content/10.1...

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

Check out long-read sequencing results in human IGH! HUGE duplications in constant gene regions...and 7 copies of IGHV3-23 on one haplotype! @lossiusandreas.bsky.social @williamlees.bsky.social www.biorxiv.org/content/10.1...

We built a new tool for disentangling local haplotypes from long-read sequencing: check out devider! github.com/bluenote-157... www.biorxiv.org/content/10.1... 1/5

I extended my fast-minimizers blogpost with the lastest results, providing proper deduplicated minimizers and super-k-mers in 1.65ns/kmer, and canonical kmers in 1.90ns/kmer. Or 5.4s and 6.4s respectively on a human genome. Let me know if you want to use this :) curiouscoding.nl/posts/fast-m...

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

Thrilled to receive the award! I highly recommend the Microbiome Virtual International Forum @microbiomevif.bsky.social to folks interested in bioinfo and microbiome, free online seminars with flexible times + very high quality talks.

Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/

I wrote about the backstory of our recently published metagenomic profiler called sylph (www.nature.com/articles/s41...), partially to celebrate the new migration to bluesky Check out the blog here: jim-shaw-bluenote.github.io/blog/2024/de... -- and I apologize in advance for the lack of brevity :)