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Major updates to MLST analysis at One Codex: we’ve expanded to 100+ species, added fungal support, and integrated long-read sequencing compatibility.
Read more about our revamped characterization workflow: https://www.onecodex.com/blog/2026/01/05/comprehensive-and-accurate-bacterial-isolate-characterization-using-multi-locus-sequence-typing/
Researchers have created over 300k plots in One Codex since the launch of our data viz features 📊
We're adding lots of new functionality (including statistical analyses for alpha and beta diversity) to Custom Plots, and would love your input: what are the most common analyses you perform?
If you've used One Codex recently, you might have noticed our new Workflows page in the One Codex application got a fresh cost of paint over the last couple of months. 🧑🎨
We’ve made it even easier to find the analyses you’re looking for, from shotgun and 16S classifications to functional analyses, AMR detection, genome assembly and more.
But the ✨real magic✨ is coming in just a few short weeks. We’re about to roll out the biggest new feature on One Codex possibly ever, so stay tuned 🍿 🧬
Every couple of weeks we have a No Stress Journal Club® 😅, where one of us leads the team through a paper from the world of microbial genomics. And now, we'll start sharing some of these with you! First up, GraphSNP from Forde et al:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05332-x
Background Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. Results GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. Conclusions GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .
One Codex’s updated bioinformatics solution for the Twist Viral Panels now supports Oxford Nanopore and PacBio, improves viral detection sensitivity, and offers customizable reporting thresholds to better fit diverse lab workflows.
We’ve just released the biggest update ever to our Antimicrobial Resistance analysis! Here are some highlights:
📈 Over 8,500 markers across 59 gene classes - a 10x increase over the previous panel
🧬 Universal compatibility with short and long sequencing reads from Illumina, Oxford Nanopore, PacBio, and ThermoFisher
🦠 Support for alignment and SNP-based marker detection
Read more in our blog post at https://buff.ly/y4ZdqNe!
Our new AMR detection workflow is now available and features over 8,500 distinct AMR sequences from 59 drug classes, an order of magnitude more than our previous database! This new workflows covers a wide variety of antimicrobial classes and resistance mechanisms.
One Codex is heading back to Boston this week for the Microbiome Movement Drug Discovery Summit!
We’ll be giving a talk on FAIR (Findable, Accessible, Interoperable, and Reusable) data and the role of bioinformatics, as well as how building a FAIR data platform at your organization can enable and facilitate ML and AI methods for microbiome research.
