Introducing 🎉sourmashconsumr 🎉, an R package that reads, parses, plots, and analyzes the outputs of the sourmash Python package. Pub: arcadia-research.pubpub.org/pub/resource-s… GitHub repo: github.com/Arcadia-Scienc… Documentation site: arcadia-science.github.io/sourmashconsum… 🧵 [1/8]

Introducing seqqc, a new Nextflow pipeline for quality control of short- or long-read FASTQ files. 🧵 [1/8] GitHub: github.com/Arcadia-Scienc…

This image from today's IPCC synthesis report is brutal. The existing policy trajectory represents a profound failure of our governments, and of our international political system. We need much more aggressive mitigation and much stronger international cooperation.

Here are the big takeaways from the IPCC Synthesis Report released today. First, climate change has already caused widespread and substantial losses to almost every aspect of human life on this planet, and the impacts on future generations depend on the choices we make NOW.

#BOSC2023 isn't just about #OpenSource -- we want to hear about your work in #OpenScience, #OpenData, #OpenStandards, and more! Abstract submission deadline April 20! open-bio.org/events/bosc-20…

Early Career Scientist? Likes Supercomputers? Likes the Sun? Come work in my group of High Performance Computing consultants at San Diego Supercomputer Center, help scientists develop, scale and run Data Intensive computations on our Supercomputers. zonca.dev/posts/2023-04-… #job #HPC #RSEng

A lovely article on STdeconvolve (software by Dr. Jean Fan lab) and how and why they made it easy to use: nature.com/articles/d4158… Fantastic points, and something I echo from my own experience. Via Tessa Pierce Ward, PhD (@bluegenes.bsky.social)

5. A new study led by @EgerAaron estimates that these benefits provided by kelp are worth at least $500 billion a year (though probably a lot more). Kelp forests of course do this for free. nature.com/articles/s4146…

🎉Just released KMCP databases v2023.05, including 85,205 genomes from GTDB r214, 496 from RefSeq-fungi, and 33479 from Genbank-viral, in a total size of 110GB. You can even choose NCBI Taxonomy or the combination of GTDB+NCBI in the profiling step🍻. bioinf.shenwei.me/kmcp/database/

There are some good papers/resources linked from here: publicengagement.umich.edu/balloon-releas… Anyone else have good resources on the environmental impact of helium balloons? Cc Dr. Jenni Brandon 🇺🇸❤️🇺🇦

👇 This is likely to be in the top-5 most important bioinformatics advances of the last decade. Think BLAST, but for structures. This makes structural bioinformatics the new mainstream.

Are you a data creator/user in #metagenomics or other #omics? We’re working on standards for fair data reuse and would like your feedback. We welcome contributions by scientists from all career stages. 5-min survey here: rb.gy/qbcsw Please RT!

#sourmash databases are now available for @ace_gtdb GTDB R08-RS214 (403k genomes)! sourmash.readthedocs.io/en/latest/data…

This is now published in Genome Research! It was accepted and presented in RECOMB Conference Series 2023. The work shows how to compute ANI using FracMinHash, currently implemented in github.com/sourmash-bio/s…. Paper: doi.org/10.1101/gr.277… Congrats to Tessa Pierce Ward, PhD (@bluegenes.bsky.social) and David Koslicki!

Happy #preptember! For #hacktoberfest, we Arcadia Science are curating a list of bioinformatics open-source repos that are accepting contributions. If you’re a maintainer comfortable with PR contributions, we would love if you would add your repo. 1/5 🧵 docs.google.com/document/d/1Ej…

It was a great pleasure to review this paper by Jim Shaw and Yun William Yu! Skani is a super fast and efficient (written in rust!) tool to compute the ANI of a query against a collection of sequences in the presence of incomplete assemblies (i.e. a common *real* case).

In 1985, Carl Sagan told Congress that continuing to burn fossil fuels will increase global temperature, cause climate change, melt glaciers and ice sheets, and cause sea level rise. Imagine if we had listened to him them. No time to wait. #ActOnClimate #climate