#bioinformatics

Busy year:

- Workflow programming for Data Analysis on #HPC Systems (Course in Mainz in January):
- Same Course in Dresden (February)
- #SnakemakeHackathon2025 at the CERN in March:
- upcoming: #OpenScience Retreat (no hashtag, yet?) in April
- International Supercomputing Conference in June (so, @boegel, I will be there, after all and hope to meet people from @irods, too ; will you be there folks from #iRODS ?)
- German Conference for #Bioinformatics and NHR Conference in September

And I do not know whether this will be all. I have a nagging feeling there is more to come

My blog gets 30K views per month. The traffic is not huge but decent. I have limited time and am not an expert on every topic. I want to do an experiment. If you are an expert and want to write a tutorial on anything bioinformatics, please message me. #bioinformatics

Big shoutout to the folks at NCBI GEO. They have been doing an incredible job managing enormous amounts of gene expression and related biomedical data for many, many years They do it efficiently and very, very well. I am so grateful: both when I download data published by others and when I submit my own data. You are true #bioinformatics heroes doing priceless and highly impactful work! #NCBI #nih

#Genomics
#Bioinformatics
#Academia

Beware US academic coders. If you have collaborators contributing code from a sanctioned region, your repos may be locked.

See https://mastodon.social/@organicmaps/114155428924741370

The kicker is that the US is leaning authoritarian and all in on censorship. If Canada or Mexico become sanction targets and you have code pushes from there, Microsoft will lock you out of your GitHub accounts.

The #SnakemakeHackathon2025 just induced another collaboration for me!

It is always good to work along with like-minded people, interested in #ReproducibleComputing, #HPC and #Bioinformatics

#OpenScience

Want to improve your genomic variant calling pipeline? Join our webinar to learn about ncbench, a powerful benchmarking tool. We'll also cover other essential genomic benchmarking topics. Register for free: https://t1p.de/o4al3 #bioinformatics #genomics #variantcalling #ncbench

Alexandros Stamatakis' annual EMBO satellite #bioinformatics workshop in Crete is open again for registration (free-of-charge, first-come-first-serve)

This year: #biodiversity #genomics tools

https://forms.gle/GRvPxCp2TnYdo8Po8

As Alexi is keen to point out: "... a good excuse to visit Crete?"

Working with newer ONT and pacbio data, I feel like minimum requirement for a proper raw data upload (to SRA and such) should be BAM calls at the very least, if not the raw signal files themselves. Either way, the fastqs just don't seem to cut it for meaningful in-depth research use.

#bioinformatics

Does anyone have any posts or past toots they could reshare about how they have setup or are working within a team in #bioinformatics, #genomics, #research etc. things that how worked or haven’t worked, organising and sharing projects and code, notes and documentation, collaboration and communication, software, network and local or cloud compute arrangement. Always find reading others experiences insightful and beneficial.

How does everyone organise all their projects on #GitHub within their teams, like projects into groups or topics? naming schemes or have you switched to #GitLab for this feature?
#research #genomics #bioinformatics

#nfcore "For more transparency and easier management of the proposals, all ideas and concepts for new pipelines will instead be submitted as GitHub issues on a new 'proposals' repository:"

https://github.com/nf-core/proposals/issues

#nextflow #nfcore #workflow #bioinformatics

2/n While our #IdeenExpo presentation from last year just covered #Windows OS, this time we presented the #AR molecular visualization system running under #Ubuntu 24.04LTS #Linux. Lots of fun explaining...
#DIYbio #lab #instruments #OpenSource #chemistry #bioinformatics #CompChem #AugmentedReality

Bioconductor Kenya Course Kickoff! Our first Bioconductor course in Africa started in Nairobi! Day 1 featured learning and collaboration with Laurent Gatto, and Michael Landi. Sessions later this week by Fabricio Almeida-Silva, Laurah Ondari, and Zedias Chikwambi. Thanks to CZI and UL Global for funding.
#Bioconductor #Bioinformatics #RProgramming #Carpentries #Africa

https://github.com/yangao07/longcallD LongcallD is a local-haplotagging-based variant caller designed for detecting small variants and structural variants (SVs) using long-read sequencing data. It supports both PacBio HiFi and Oxford Nanopore reads. #sv #structuralvariant #calling #mapping #bioinformatics

(via Heng Li on twitter)

"BWA-0.7.19 released with a fix to the internal HD-line bug introduced in 0.7.18"

https://github.com/lh3/bwa/releases/tag/v0.7.19

#bioinformatics #bwa #mapping

Yikes modkit likes to eat up ram when making summaries of methylation called bams.

Subsampled bam with 100k reads still requires close to 50gb of ram, which for me is cutting it way too close. I'm beginning to envy those real lab people with monster rigs.

#bioinformatics

SciTech Chronicles. . . . . . . . .Mar 24th, 2025

https://bit.ly/stc032425

#genes #chromosome #hippocampus #myelin #Aardvark #multimodal #GFS #democratising #cognitive #assessment #Human-AI #Collaboration #E2A #192Tbit/s #Alcatel #2028 #genomics #bioinformatics #antimicrobial

Dorado polisher supporting 'any HTS file type' alongside the assembly input is a bit misleading. From what I can tell it only runs on reads containing model information under @RG tag. So it essentially limits your option to Dorado generated BAM file and nothing else.

#bioinformatics

I like to remind people, if you want less of my human rights, future, open science, and other opiniatied posts, follow my #cheminformatics and #bioinformatics account at @egonw@social.edu.nl

Of course, I love you to stay here too, because I honestly believe in a better future and am hopeful. But hoping is not enough, hence my posts here.

Looking at a funny discrepancy between Dorado 0.8.3 methylation-SUP basecalled bam vs 0.9.1 methylation-SUP basecalled bam.

They're the same raw files with same models, only Dorado version are different.

Left, 0.8.3, right, 0.9.1

That looks like one heck of a discrepancy for a few version numbers on basecalling software.

#bioinformatics #nanopore