Ultrafast identification of signature sequences in microbial genomes

Reference-free, privacy-preserving wastewater pathogen surveillance for federated hospital networks. DNABERT-2 embeddings + Transformer-encoder VAE detect emerging anomaly clusters in unclassified reads. AIxBio Hackathon Track 2, Apart Research.

Functions for working with NCBI's Pathogen Detection data

Pathogen Identifier and Strain Tagger datasets

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

Circulating fungal rRNA detection

ZoonomiX is a bioinformatics pipeline for analyzing microbial genomes, detecting pathogenicity, resistance genes, and mobile elements, and assessing zoonotic risk using BLASTn.

🐹 Metagenomic Alignment and Reporting for Monitoring Of Threats