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.

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…

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

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

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.

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.

A snakemake workflow for amplicon sequencing

Repositorio del curso "Vigilancia genómica de S.pneumoniae y S. agalactiae"

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

Backend routines for genomic surveillance data processing of Rede Genomica Fiocruz

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