As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41... #HumanGenomics #Pangenomes #ReferenceGenomes

Did not expect to see disk space become an issue but after a disk clean up and restart I ended up with 243 and 244 gbp for these two @nanoporetech.com flowcells 🎉🚀🧬 💚🟩💚🟩💚🟩

I am looking to get my hands on some #Illumina 5-base methylation data - does anyone have a bam file that I could use for some testing? Please RT for reach!

My current favorite strategy for using LLMs to code (specifically, GitHub Copilot agent mode) is to write a paragraph or more of instructions, and finish with "Do not start writing any code yet. First, tell me all the questions you still have about this plan".

Why yes Windows, I did want to save this email attachment in C:\Users\pbayer\AppData\Local\Microsoft\Olk\Attachments\ooa-6b0f86af-a548-4060-9a83-7d943fcaa440\157ef8591494ef374d2433d75c318962f8bc4054af4a1be24c8e02b89b6d5ec9 that's just a logical place for it

(forgetting the word for antibiotics) do i need cancel culture

Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.

We are hiring a postdoctoral researcher to identify genes involved in frontotemporal dementia using short- and long-read sequencing data. More information is available at jobs.vib.be/j/124543/pos....

NEWS! Nation capable of spotting spurious link between paracetamol and autism still baffled by obvious link between guns and mass shootings

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2...

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

This is awesome. @ellecordova.bsky.social

Which tool should I use nowadays to identify pathogens in long-read DNA sequencing from human brain samples?

Ok this is mad "...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste" www.nature.com/articles/s41...

Facts

For @nanoporetech.com geeks I’ve just been pointed at this very helpful site - nanoporetech.github.io/ont-output-s... - I hadn't seen this before and it's very useful!

Could you send me a Zoom link? Is Teams okay? The new coke vs. pepsi question.

Coukd It Have BEEN Found With Short Reads? 🧬🖥️ omicsomics.blogspot.com/2025/06/coul...

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.

This would be a great time for everyone to be cool when reviewing manuscripts and *not* request $25,000 worth of new experiments that don’t substantially advance or validate the study...

🚨 Training Alert: Dive into long-read single-cell RNAseq with #scywalker 🗓️ June 5, 2025 📍 Ghent – VIB/UGent FSVM II 🎟️ Registration deadline is Monday May 26th: https://training.vib.be/all-trainings/scywalker-processing-long-read-single-cell-rnaseq-data

Our spotlight winner, Ruben Cools, presented his full talk exploring how they are bridging genotype and phenotype through long Oxford Nanopore read, single-molecule multiomics. #NanoporeConf

If only I could use such an incredibly wide screen to browse long reads on IGV #nanoporeconf

Everyone in the past was neurotypical, which is how we got things like this single-author, eight-volume encyclopedia of ferns

✨ We’re off for three days of next-generation sequencing at #RNGS25 in Antwerp! Experts from academia and industry will showcase innovations transforming healthcare, agriculture, and more. 🎤 Kicking off: Rosa Rademakers on GOLGA8A repeat expansion & its link to FTD. Stay tuned! 🔬 #Genomics

About fifty years ago, NASA strapped a message in a bottle to a rocket and flung it into the deep dark It wasn’t supposed to go this far, but it did. Long past its mission, it’s still out there so far away now that a simple hello takes a day to reach it, and another day to hear if it says hello back

Last 2 days left to register for #RNGS2025. ⏱️So, don't miss out and register! Catch Simon Koplev's talk on the use of long reads for rare disease research. 📅19-21 March 2025 📍Antwerp, Belgium vibbio.tech/4htR01q #NGS #genomics #sequencing #omics

🚨The final deadline to register for #RNGS25 is this Wednesday, March 5th!🚨 Make sure to register - You don’t want to miss Prof. Bernard Thienpont (@bernthie.bsky.social)'s fascinating talk on improving patient care by using cell-free DNA methylome analysis.🧬 www.vibconferences.be/events/revol...

How many times per day can one check the manuscript status page before it becomes excessive? Asking for a friend.

Every scientist, long before they were a scientist, was a little kid who stood in front of a fish tank or stared up at the stars or turned over a rock to look at the bugs underneath and said “wow”. On the best days, working in science still feels like that.

📢 Our lab is looking for a bioinformatics postdoc. We have lots of exciting projects to work on, including single cell (epi-)genomics, microglia xenotransplantations and nanopore long reads splicing analysis. Look out for the official advert next week and get in touch in the meantime 🧬🧠

Yes, they can hallucinate papers that don't exist, discuss results that seem to be imaginary, and can be confusing and inconsistent. But talking to tenured professors may still be helpful

Utilitarianism - never use "utilised" if you can just say "used"

Let us introduce ourselves: blog.vib.be/there-is-mor.... NSF is a competence facilty, which means we are bunch of researchers and scientists that are driven by colaboration and technical expertise

We are hiring a bioinformatician/data manager! Please share within your networks :-) jobs.vib.be/j/99863/bioi...

Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity https://www.biorxiv.org/content/10.1101/2025.01.06.631535v1

Is there anyone who already started running PacBio's new SPRQ chemistry? Our Revio will be updated in a couple of weeks but I’m really curious to know how it’s working at other sites 🧪🧬

The reviews that Wouter v2024 promised to do are now a problem of Wouter v2025.

Many academics point to bioRxiv as “the one thing improving science publishing”. If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2

What's a reasonable price to sequence a 96 well plate of ~3.5MB bacterial genomes to high quality? Links to service providers (especially but not uniquely in Oz) welcome! Please repost.

I have made a new release of kyber, a tool to make a quick sketch of your long-read sequencing data or to compare multiple datasets. It uses a fixed grid of accuracy and read length. Now also supports ubam - feedback appreciated! github.com/wdecoster/ky...

Releasing a new version of cramino, a fast tool to get summary metrics from your (long read) bam and cram files. v0.14.1 will additionally output the modal accuracy, support for reading from stdin and remote files, and is about 2x faster for cram files. More on github.com/wdecoster/cr...

Is there something like a human pangenome browser where I could search by GRCh38 coordinates or gene name and see what the graph looks like for my messy region of interest?

Whoa! Getting a 10x speed up and 10x reduced memory use by limiting which sam_fields must be decoded from a cram file 🤯

There's a ~1000nt sub-viral RNA that shows up on every continent, and in humans, and it seems to have gone unnoticed! It has no sequence similarity to any database and codes for a wacky protein Super happy to finally share my thesis work on "Obelisks" tinyurl.com/yc54fzj9 #MicroSky #microbiomesky

A refreshing type of bullshit nonsense: my 13-inch laptop screen is deemed too small to load the Peer Review Form to complete the review for a manuscript. The alternative is to mail the editor to request the form to complete it offline.

PSA: if you want people to complete your survey, don't make it a 20-minute survey.

Not sure who needs to hear this. Anyway: Reviewers often do their work in train or airplane seats or similar confined locations. So they like it when figures, captions& associated text are close together in a manuscript. And authoring technology has sufficiently progressed since the typewriter era.

I'm pleased to announce the release of HiPhase v1.0.0!  In addition to phasing small and structural variants from #PacBio #HiFi datasets, HiPhase now also includes support for phasing short tandem repeats (#STR) at the same time!   Full release notes can be found here: github.com/PacificBiosc...