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VENAE is a bioinformatic workflow that rapidly identifies bacterial and fungal organisms and their antimicrobial resistance (AMR) determinants from positive blood cultures using Oxford Nanopore long-read sequencing. It generates a clinician-friendly HTML report to support timely clinical decision-making.

A platform combining BRC-Analytics for pathogen genomics, an agentic AI assistant, and standalone JupyterLite notebooks to standardize and reproduce RNA-seq analysis of critical fungal pathogens like Candidozyma auris.

CUPID is a computational pipeline designed to link antimicrobial resistance genes to their specific bacterial hosts and genomic context using methylation patterns derived from Nanopore metagenomic sequencing data. It extends association analysis from assembled genomes to individual contigs and reads to improve accuracy in clinical surveillance settings.

AMRgen is an R package designed for systematic antimicrobial resistance (AMR) genotype-phenotype analysis. It integrates genomic and antimicrobial susceptibility testing data to model and visualize associations between AMR genes and resistance phenotypes.

HCVTyper is a comprehensive Nextflow pipeline designed for the analysis of high-throughput sequencing data related to Hepatitis C Virus (HCV). It supports genotyping, de novo assembly, taxonomic classification, and detection of antiviral resistance-associated variants (RAVs).

AMPSeek is a workflow designed to predict the antimicrobial activity, toxicity, and three-dimensional structure of candidate antimicrobial peptides using in silico methods. It integrates several specialized tools (AMPlify, tAMPer, LocalColabFold) into a single command-line framework for efficient high-throughput screening.