Registration for the International Genome Graph Symposium 2024 is now open at iggsy.org. Join us in Ascona for a great lineup of speakers and come to present your work. #iggsy24

Last chance to send your abstract to the International Genome Graph Symposium 2024 in Ascona! More info at iggsy.org
Keynotes include Arang Rhie Ben Langmead Camille Marchet @[email protected] Eimear Kenny Ewan Birney Jasmijn Baaijens Kateryna Marinka Zitnik Zamin Iqbal #iggsy24

Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline. github.com/KolmogorovLab/…

Our CARD pilot paper with Kimberley Billingsley Cornelis Blauwendraat Benedict Paten and many others is online! We establish a wet + dry lab protocol for single nanopore flow cell sequencing, which generates state-of-the-art SNP and SV calls + assemblies. rdcu.be/dl901

A new set of Oxford Nanopore sequencing protocols, implemented in an Alzheimer's research project, will open up previously inaccessible regions of the genome with medically relevant variations. This is a huge step forward for large-scale genomics projects! 🎉
ucscgenomics.sites.ucsc.edu/2023/09/14/new…

Excited to share our collaboration with Dean lab National Cancer Institute! With long reads we sequenced a panel of cervical + head and neck cancer cell lines with complex SVs and aneuploidy. In particular, breakage-fusion-bridge (BFB) amplifications were ubiquitous (1/n) medrxiv.org/content/10.110…

We are deeply saddened by the loss of Michael Ashburner, a pioneering co-founder and former Head of Research at EMBL-EBI.

His contributions to bioinformatics have been immeasurable. Our thoughts are with his family, colleagues and all those whose lives were enriched by his work.

Pangene is a new tool for constructing a pangenome gene graph from multiple assemblies: github.com/lh3/pangene. You can explore the rich haplotypic diversity of human genes at pangene.liheng.org. Still WIP.

In a new paper with Jyotshna Rajput and Ghanshyam Chandra, we developed new algorithms for co-linear chaining on cyclic pangenome graphs. To appear in WABI

biorxiv.org/content/10.110…
github.com/at-cg/PanAlign…

A group of us have been thinking about how to explore human pangenome scale data and make them easier to understand for while. Great collaboration with Genome in a Bottle Fritz Sedlazeck Asif Khalak Sairam Behera.

twitter.com/naturemethods/…

Preprint on hifiasm ultra-long (UL) integration for better assembly. Now hifiasm works with

HiFi
HiFi + UL
HiFi + trio/Hi-C
HiFi + UL + trio/Hi-C

One executable and mostly one command line. Work by Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren. Help from HPRC and T2T.

Our latest methods paper 'Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation' (aka MashMap3) is out with Bryce Kille Erik Garrison Todd J Treangen! There's an interesting backstory here 🧵 \ biorxiv.org/content/10.110…

'Rare penetrant mutations confer severe risk of common diseases' medrxiv.org/content/10.110…

As #PublicServiceRecognitionWeek comes to a close, I want to shout out my fellow Terp and Maryland resident, Adam Phillippy.

He is one of 13 Maryland finalists for The Partnership's Samuel J. Heyman Service to America Medals -- the sort of Oscars for public service workers.

The Human Pangenome Reference Consortium - the 3rd chapter. For an intro into the human pangenome, check out this thread - twitter.com/ewanbirney/sta… - and additional papers - twitter.com/ewanbirney/sta… but now on to the weirdest 'our genome does that!' moment. Brace yourself for genome geekery

Pangenome graph construction from genome alignments with Minigraph-Cactus go.nature.com/3nXfcmt

We're ✨revolutionizing✨the human genome reference. The #HumanPangenome Consortium, co-led by UC Santa Cruz, has just published a draft of a more robust, diverse, and complete reference. This will be a game-changing resource for genomics & health research news.ucsc.edu/2023/05/pangen…

Researchers from the National Human Genome Research Institute-funded Human Pangenome Reference Consortium (@HumanPangenome) have completed a collection of new human reference genome sequences that much more accurately reflect global diversity! genome.gov/pangenome

My favorite T2T/Pangenome discovery so far: a multi-megabase inverted segmental duplication on the short arm of chr14 that explains the mechanism of Robertsonian translocations. Great writeup by Stowers Institute 'Answering a 50-year-old mystery' stowers.org/news/investiga…

Congratulations to the Human Pangenome Reference Consortium - in particular Benedict Paten for his leadership + highlighting Ensembl's role via Fergal Martin in annotation. For the rest of this thread I will explain this technical genomics tour de force using... Shakespeare nature.com/articles/s4158…