Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow https://www.biorxiv.org/content/10.1101/2025.10.03.680343v1

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper. #Metagenomics #MicrobialCommunities #Bioinformatics @natbiotech.nature.com 🧬 🖥️
www.nature.com/articles/s41...

TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection. #Metagenomics #Sequencing #PathogenDetection #Bioinformatics @biorxiv-bioinfo.bsky.social
www.biorxiv.org/content/10.1...

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

NIH just early-expired its 1st & only software NOFO: “Building Sustainable Software Tools for Open Science.” Our proposal supported lab automation software infrastructure, with backing from major robotics companies. I guess “sustainable” is too risky now. So much for funding the STEM workforce.

DIAMOND v2.1.11 is now available, providing numerous improvements and fixes. github.com/bbuchfink/di...