We open our second day at #Hitseq @hitseq.bsky.social with our last key note speaker Tobias Marschall and his insightful talk about the human pangenome and the challenges for structural variation analysis. His work has focused on tackling current limitations such as sample size and remaining gaps

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Sassy solves approximate string matching: finding all matches of a pattern in a text.

Sassy is out now!

Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!

Available now wherever you get your code

With @rickbitloo.bsky.social

curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...

@denbi.bsky.social will offer 3 #workshops at @gcb-bioinformatics.bsky.social 2025, focusing on #cloudcomputing, #pangenomics and #protein structure analysis. For more information see: www.denbi.de/news1/1904-d...

🧬🖥️
📝 To-Do List for #GCB2025:
✅ Check the programme: gcb2025.de
✅ Submit your poster
✅ Buy your conference ticket
✅ Book your hotel room
✅ Take advantage of the DB event offer and travel to Düsseldorf by train at a discounted rate, more info here: gcb2025.de/GCB2025_venu...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

🆕 New Features
• Re-rendering of HTML
• Plug in your own reports with !Custom
• Download plots as PNG or SVG
• Select hexagons in NodeDistribution 🔷 and download node ids!

🐞 Fixes & Improvements
• 🐌 Faster similarity calculation
• 🔧 Cleaner YAML syntax
• 🔁 Better handling of dependent analyses

GitHub - codialab/panacus: Panacus is a tool for computing statistics for GFA-formatted pangenome graphs Panacus is a tool for computing statistics for GFA-formatted pangenome graphs - codialab/panacus

🚀 Panacus v0.4.0 is out!
Bringing more power, flexibility, and speed to your pangenome reports 🧬📊

👉 Upgrade now & explore: github.com/codialab/pan...

#genomics #bioinformatics #pangenome #panacus

Reconstructing rearrangement phylogenies of natural genomes - Algorithms for Molecular Biology Background We study the classical problem of inferring ancestral genomes from a set of extant genomes under a given phylogeny, known as the Small Parsimony Problem (SPP). Genomes are represented as se...

Improved method for inferring ancestral genomes! We introduce a powerful ILP for the Small Parsimony Problem under a complex rearrangement model that handles duplications & indels. Big gains in accuracy & runtime on real and simulated data! #Genomics #Phylogenetics
doi.org/10.1186/s130...

Verkko2 integrates proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding. #LongReads #HiC #GenomeAssembly #GenomeScaffolding #Bioinformatics @genomeresearch.bsky.social‬
genome.cshlp.org/content/earl...

🧬 & 🖥️
📢Call for Posters #GCB2025 | Join the #bioinformatics and #computationalbiology community at the German Conference on Bioinformatics! Submit your poster now!
Important Deadlines:
📌 Early Bird Registration: 5 July 25
📌 Poster Submission: 7 August 25
🔗 gcb2025.de/GCB2025_call...

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Human readable compression of GFA paths using grammar-based code Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying grap...

New in pangenomics: We extend the GFA format to represent haplotype paths in a compressed yet human-readable way. Our tool sqz (/ˈskuzi/) achieves 40× compression on chr19 with 1000 haplotypes, plus 10× faster analysis and 8× lower memory use.
🔗 www.biorxiv.org/content/10.1...
#bioinformatics

Submit your abstracts from all areas of #bioinformatics and #computationalbiology for the German Conference on Bioinformatics - #GCB2025 at University of Dusseldorf from 22 - 24 September 2025!
abstract submission: gcb2025.de
@denbi.bsky.social @openbio.bsky.social @SIB.mstdn.science.ap.brid.gy