The One Codex Blog Posts about epidemiology

New features: Whole genome clustering and BaseSpace integration

Today we’re happy to announce two new features for all users on One Codex: whole genome clustering and integration with Illumina’s BaseSpace. The first opens the door to new types of analyses, while we hope the second will allow many to spend less time moving their data around and more time exploring it! Whole (meta)genome clustering In addition to our previous sample comparison tool, we’re very excited to announce that One Codex now supports arbitrary, interactive exploration and clustering of your isolates and metagenomic samples.

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Automated MLST annotation

Today we added automated Multi-Locus Sequence Typing (MLST) to One Codex. MLST is a powerful epidemiological tool that is based on curated collections of conserved mutations in core marker genes. This common reference standard is used to differentiate closely-related isolates of the same species, with many common species having hundreds or thousands of defined MLST profiles. Datasets that are identified as being isolates or single-genome assemblies will be automatically analyzed and tagged with the detected ST label.

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