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.

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

A snakemake workflow for amplicon sequencing

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

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…

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.

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.

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.

Syed Adnan Haider pathogen genomics blog

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

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

GitHub profile README for Syed Adnan Haider

Global viral genomic surveillance dashboard — real-time outbreak monitoring, interactive maps & public API for 50+ pathogens (COVID-19, Ebola, dengue, avian flu, mpox). An independent open-science project. → infectonet.org

Reproducible post-culture whole-capsid Illumina workflow for poliovirus. Reference-based consensus, antigenic site analysis across VP1-VP3, phylogeny, and optional de novo checks.

A Nextflow pipeline used to analyze sequencing data and perform analysis on captured sequences