Realized that I released a couple of new tools last week and didn't announce anything. The first one is *dupblaster*. Samblaster inspired streaming queryname grouped duplicate marking for NGS reads: github.com/fulcrumgenom...

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

Our paper on Trimmomatic v0.40 is officially published in Bioinformatics! A decade after the original, the ~50,000-times-cited NGS trimmer gets a major overhaul. Here's what's new 🧵 doi.org/10.1093/bioi... #Bioinformatics #NGS

Fantastic to see this work published, congratulations to all co-authors! It further validates the value of structural variants (SVs) as biomarkers for cancer liquid biopsy, as implemented in SAGA Diagnostics' Pathlight MRD test. #ctDNA #MRD #LiquidBiopsy #PrecisionMedicine #BrCa #BreastCancer

Excited to announce we’ve constructed a complete, haplotype-resolved assembly of a human pancreatic cancer genome. By comparing tumor cell line and normal tissue assemblies directly, we developed phased somatic benchmarks. Thanks to many in GIAB! www.biorxiv.org/content/10.6...

We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...

There's an opening in our CompBio group at #PacBio. Apply below if you're interested in method / tool development for long-read sequencing applications! #Bioinformatics pacbio.wd12.myworkdayjobs.com/PacBio-/job/...

Hiring Senior Computational Postdoc to lead large-scale scRNAseq analysis for Project JAGUAR, one of the world’s most comprehensive single-cell immune resources from Latin American ancestries. If big data, global partnerships, human diversity and immune regulation excite you, apply! bit.ly/3XyFWrW

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Calling cancer data scientists! 📊 💽 🧮 We have a number of open positions in our core facility @icr.ac.uk These are bioinformatician staff scientist like roles to work on exciting single cell, spatial & other genomics data from across our Institute. A PhD is required. jobs.icr.ac.uk/vacancies/13...

Opportunity! Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)

Conda in the Packaging Spectrum: From pip to Docker to Nix If conda is a distribution, where does it fit alongside pip, Docker, and Nix? Part 2 of the 3-part series! 🚀 #conda #packaging #python conda.org/blog/conda-p...

The Cluster of Excellence @greenrobust.de is hiring: - Computer Scientist/Research data manager: shorturl.at/xSvvO - Data steward: shorturl.at/l6NCv - Scientific coordinator 'Plant Perturbation Atlas': shorturl.at/vBU6x Deadline: Friday, 7 November 2025 RT are welcome #plantjobs #plantscijobs

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

A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing. www.uu.se/en/about-uu/...

📣📣 Cool job alert! The @bakerresearchau.bsky.social is recruiting up to 2 new PIs in Biomedical Data Science 👉 www.seek.com.au/job/85989791... You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁

📣 🥳 🧑‍💻 Our department is hiring: Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark Deadline June 1st Thanks for sharing! mbg.au.dk/en/news-and-...

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...

🚀 Truvari v5.0 is here! 🎉 What’s new? 🔹 Enhanced symbolic variant support for <DEL>, <DUP>, <INV> 🔹 Robust BND comparison for cross-representation SV matching 🔹 Improved SV sequence similarity & HUGE SV support 🔹 Cleaner UI & Revamped API 👉 More: github.com/ACEnglish/tr... #Genomics #Bioinformatics

#ICYMI our deep dive into ALK1 biology, at the intersection between angiogenesis and immunology with clear implication for the targeting of immunomodulatory cues & cancer therapy!

BRCA1 turned 30 🎉 To celebrate, Jos Jonkers and I explored three decades of BRCA1 research - what we’ve learned about its biology, its role in tumorigenesis and future directions to improve the life of BRCA1 mutation carriers. Now out in Cancer Discovery ⬇️: aacrjournals.org/cancerdiscov...

Our first curated draft somatic structural variant benchmark for the new GIAB PDAC tumor cell line HG008-T is at ftp-trace.ncbi.nlm.nih.gov/ReferenceSam..., based on extensive short+long read sequencing data described in doi.org/10.1101/2024.... Feedback to improve future versions is very welcome!

Regular abstracts from #SABCS24 are out! 3407 pages of new breast cancer discoveries. Find them here: sabcs.org/Portals/0/Do...

WOOT! Just in time for #SABCS24 looks like @sabcs.bsky.social is officially on BlueSky! cc: @maryamlustberg.bsky.social @drsgraff.bsky.social @stage4kelly.bsky.social @amjohnston.bsky.social @amybeumer.bsky.social @raalbany.bsky.social @hoperugo.bsky.social

Dear Colleagues, For all of you in BlueSky, Greetings, We are Now Here!! We invite you to Join & Follow OncoAlert at @oncoalert.bsky.social Thank you for your support!

For the #cancer / #oncology folks, OncoAlert is now on bsky: @oncoalert.bsky.social

in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods go.bsky.app/GmS1cH

Inspired by the other amazing starter packs - here's one for cancer researchers! I tried to make this broad - from immunology to genomics to cell biology and so much more.. This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺 Hope its useful! go.bsky.app/FEoaJMc

I've created a Breast Cancer Starter Pack covering clinical oncology and research. Please share, and let me know in case you'd like to be added. #brca #breastcancer go.bsky.app/6KXpPSy

We are actively recruiting for two open Computational Biology positions in our NGS group - both covered by this listing www.ginkgobioworks.com/job-listings...

Happy to have contributed a small part to this study. "Ultrahigh" #HER2 copy number by #dPCR or #RNAseq signals poor response to adjuvant #trastuzumab in breast cancer.

Online Hackathon to improve the annotation of @galaxyproject.bsky.social resources for microbial data analysis (and beyond): galaxyproject.org/events/2024-... 📆 Date: March 11th - 15th 📍 Location: Online via Zoom & chat. 2 daily stand-ups 👥 Participation: Free. Open to anyone, anywhere

Still a week to apply for this postdoc position to work with us on deep learning models for regulatory genomics 👇🏼

We will have a job ad for Japanese ecologists coming soon - any tips on breaking into the Japanese cluster here (i know its pretty big)? Good feeds or anything I can pop up in? (Other than, obviously, posting in Japanese).

Interested in breaking all your bioinformatic pipelines? Look no farther: https://gatk.broadinstitute.org/hc/en-us/articles/6012243429531-GenotypeGVCFs-and-the-death-of-the-dot

Anyone know a commercial #lab running the #BioRad MSI ddPCR kit on plasma samples? Europe preferred but not mandatory. #dpcr #ddpcr #moleculardiagnostics #cancer

For 2024, I'm going to use this flow-chart to prioritise requests to review papers. At the end of the year I'll let you know the numbers in each category. I thought of adding an "am I being paid?" question, but what's the point?

Job Alert! We are looking for a Principal Bioinformatics Research Scientist with extensive experience in large-scale microbial genomics to create and direct our new Microbial Computational Genomics and Bioinformatics Lab @StJudeResearch stjude.wd1.myworkdayjobs.com/stjude/job/M...

New Samtools, Htslib and Bcftools 1.19 releases available. github.com/samtools/sam... and co. #bioinformatics 🧪

Join our Oslo Centre for Biostatistics and Epidemiology as a full-time, permanent researcher in biostatistics or epidemiology. Application deadline Jan 15. Please see link for details. Looking forward to welcome *you* as our new colleague! 😊 www.finn.no/332286414

Job: Research software/data engineer for a short-term project building pipelines for a field + lab research project. We use #rstats, the {targets} framework, GitHub Actions, + Web APIs like AirTable, Google Sheets, + Open Data Kit. $50-60/hour, ~12 weeks full-time, remote. bit.ly/eha-rse-ad

Not enough people know about bioicons.com Open source vector graphics. Free alternatives to BioRender.

The #gnomAD team is proud to announce the release of gnomAD v4! The v4 dataset includes 730,947 exomes & 76,215 genomes, which is ~5x larger than the v2 & v3 releases combined, & includes nearly 120K indivs of non-European genetic ancestry broad.io/gnomad #ASHG23 (1/11)

Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by Kishwar Shafin which built off a framework by Pi-Chuan Chang. (github.com/google/deeps...)

There are somewhere between 5000-7000 monogenic, CNV, and chromosomal disorder. Many are ultra-rare. There are specific ICD-10 codes for a little over 500 of them. 🧬🖥️ Epidemiology challenging. Hard to estimate how many people are affected.

Reminder: you can use your own domain as account handle on bsky! Settings -> Advanced -> Change handle -> I have my own domain You only need to add a TXT record to your domain's DNS.

Exciting news! The Berlin Institute of Health at Charité @berlinnovation is launching its BIH PhD Program, focused on medical translation & innovation. 🌟 Fully funded doctoral positions for translational projects 🌟 Open for applications until Nov 22 Join us in Berlin! bihealth.org/en/notices/b...

Our lobular 'bootcamp' video is up! In addition to great scicomm content on researcher - patient/advocate interaction, we cover basic cancer biology and breast cancer 101. youtu.be/ZeQY-HEFoHU

One week left to apply for junior faculty positions in the Data Driven Life Science program in Sweden! Competitive startup, big program with a strong peer+mentorship networks, great country with strong science, international vibe and nice quality of life. www.scilifelab.se/data-driven/...

A good summary of the current work to develop the future of the Variant Call Format as we move towards millions of genomes in multiple places - help very much welcome! www.ga4gh.org/news_item/sc... #genomics #ga4gh