Nextstrain build for dengue virus

Workflow for RSV analyses on Nextstrain.org

Scripts. config, and snakefiles for seasonal-flu nextstrain builds

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.

SARS-CoV-2 variant growth rates and frequency forecasts

Nextstrain build for mpox virus

An open-source project to create a centralized hub for live streaming content.

Nextstrain build for Zika virus

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Nextstrain build for measles virus

Nextstrain build for novel coronavirus SARS-CoV-2

A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

This repository contains all changes made to the strain specific models of Corynebacterium striatum.

Pathogen Informatics Center: Analysis, Networking, Translation & Education

Mycobacterial pipeline

metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples

Repository containing lists of all published ancient metagenomic (and related) samples and libraries