Benjamin J. Buchfink

nr database @NCBI hits one billion sequences 🤩

🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... Thank you to all bug reporters and contributors! github.com/oschwengers/ba…

DIAMOND v2.1.17 has new output fields sRANK to print taxonomy nodes of the given rank associated with the subject sequence, where RANK can be any rank in the NCBI taxonomy, e.g. sdomain, skingdom, sphylum, sorder, sgenus, sspecies, etc. github.com/bbuchfink/diam…

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research (1/8) biorxiv.org/content/10.110…

HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements. #EndogenousViralElements #EukaryoticHostGenomes #Genomics #Bioinformatics academic.oup.com/bioinformatics…

Sup' #python #bioinformatics ! Didn't announce it so far, but now that it's working, I'm pleased to say you can now pip install BLAST+ (and more)! Technicalities below🧶 1/12

DIAMOND v2.1.15 now supports all taxonomy features for BLAST databases, and support for using BLAST databases has also been added to the Bioconda version github.com/bbuchfink/diam…

🚨 BREAKING NEWS: Breast & Formula Fed Toddlers Linked to Autism Diagnosis 🚨

Predicting functions of uncharacterized gene products from microbial communities go.nature.com/435C4lp

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow biorxiv.org/content/10.110… #biorxiv_bioinfo

CluSeek: Bioinformatics Tool to Identify and Analyze Gene Clusters biorxiv.org/content/10.110…

New preprint shows that DALI, TM-align and Foldseek overestimate protein structure alignment significance by 5-6 orders of magnitude biorxiv.org/content/10.110…](biorxiv.org/content/10.110…

TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection. #Metagenomics #Sequencing #PathogenDetection #Bioinformatics @biorxiv_bioinfo 🧬 🖥️ biorxiv.org/content/10.110…

It has been a while… but an updated, faster & more accurate version of OrthoFinder is now out! Scales to thousands of species on conventional compute resources with higher accuracy than ever before and the same data rich fully phylogenetic outputs 👉biorxiv.org/content/10.110…

Out in @NatureBiotech: 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. doi.org/10.1038/s41587… A 🧵

We have a new version of OrthoFinder: biorxiv.org/content/10.110… Faster scaling to larger species sets, phylogenetically resolved orthogroups, reduced RAM usage. Thanks to @dr_belcher, Yi Liu & Jonathan Holmes who have joined the team, and as ever OrthoFinder's PI @Steve__Kelly!

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

NIH just early-expired its 1st & only software NOFO: “Building Sustainable Software Tools for Open Science.” I guess “sustainable” is too risky now. So much for funding the STEM workforce.

Our proposal supported lab automation software infrastructure, with backing from major robotics companies. It was due in a week. Pure idiocy. grants.nih.gov/grants/guide/r…

The saddest thing about this is academic science doesn’t reward software development, and many fields have serious tech debt that’s a huge drag on scientific productivity.