genomic-surveillance

Estimate growth rate advantage of SARS-CoV2 variants of concern based on international genomic surveillance data and multinomial spline fits

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

VIPER is a user-friendly software for assembling and identifying viral genomes (currently SARS-CoV-2, Dengue, and Influenza), from Illumina sequencing data generated through genomic surveillance.

Automatic robot for web scraping data from Pathogen Watch website using a RESTful API and MongoDB to store and manage the scraped data.

MpoxRadar frontend codebase: an interactive dashboard for genomic surveillance of MPXV.

A snakemake workflow for amplicon sequencing

Since May 2021 the PPI Data & Analytics team has been cleaning, analyzing, and visualizing data from GISAID, FIND, WHO, and Our World In Data. In collaboration with the team at FIND we have developed a series of maps that describe next-generation sequencing capacity. The main outputs were code, data repositories, and visualizations that appear o…

Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️

A WDL-based workflow for profiling Klebsiella & E. coli genomes using Kleborate. Supports local execution with Cromwell both local & cloud deployment in Terra, enabling automated analysis of assemblies with docker & integration with Terra data tables for scalable genomic surveillance.

Repository of the course "Genomic Surveillance of S. pneumoniae and S. agalactiae

HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.

Python package and command-line toolkit for managing, integrating, filtering and annotating metadata tables.

Shiny app for the visualization of SARS-CoV-2 epigenetic data. This application presents Cameroon’s SARS-CoV-2 response through laboratory diagnosis and sequencing.

Bayesian phylogeographic reconstruction and interactive visual analytics of Zaire, Sudan and Bundibugyo ebolavirus spread in the Great-Lakes basin

Portable WDL/Cromwell workflow for microbial case-control GWAS from paired-end reads, producing annotated pyseer associations & HTML reports.

R package for pathogen lineage frequency dynamics, growth-advantage estimation, and short-term forecasting from genomic surveillance counts

RutiSeq-nf is intended for the classification, clustering and SNP barcoding of Mycobacterium tuberculosis genomes for outbreak surveillance.

Documented, correctable comparison of bacterial and viral genomic-surveillance platforms: every value backed by a cited source and a verbatim passage. Corrections via pull request.

Using Nanopore technology and AI, we contribute to developing genomic surveillance strategies at the intersection of human, animal, and environmental health to empower our understanding of pathogens, their transmission, drug resistance, and virulence—in the context of food safety, water and air quality, and human clinical monitoring.

Routine clustering for genomic surveillance