genomic-epidemiology

Pathogen NGS Documentary

Nextstrain build for mpox virus

Official place for proposals and details around monkeypox virus lineage designations

mGEMS Genomic epidemiology with mixed samples

Nextflow pipeline for species-specific typing of bacteria

Nextflow pipeline for bacterial clustering and linkage detection based on core genome analysis, designed to support genomic surveillance and outbreak investigations

Nextflow pipeline that integrates reference-based SNP calling, recombination filtering, and pangenome analysis to detect genetically linked isolates, designed for bacterial genomic surveillance and outbreak investigation

Screen plasmids for carbapenemase resistance genes, and classify using MOB Suite

BA.2.86 project with Sigal lab

Efficiently store FASTA sequences in sqlite compressed with sidecar zstd dictionary

Data used for analyses in "Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China" (Lu et al., Cell, 2020) https://doi.org/10.1016/j.cell.2020.04.023

Scripts and data for the CoVaRR-Net Pillar 6 notebook

A GLUE project for Rabies Virus (RABV).

Data used for analyses in "Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California" (Deng et al., Science, 2020) https://doi.org/10.1126/science.abb9263

Automated genomic analysis of SARS-CoV-2 sequence data

Code for the analysis and data visualization found in the paper entitled "Genomic epidemiology of dengue virus 2 and 3 reveals repeated introductions and exportations of several lineages in Colombia."

Cluster Investigation & Virus Epidemiology Tool

rMAP-Candida is a reproducible WDL/Cromwell pipeline for paired-end Candida genome analysis, integrating read QC, trimming, Kraken2/Bracken species typing, assembly, genome completeness assessment, fungal antifungal-resistance screening, species-aware phylogenomics, SNP-distance epidemiology & an HTML surveillance report for public-health genomics

Gallery for GEViT Project

Local-first, browser-based phylogenetic tree viewer for Auspice JSON and Newick files, with rooted and unrooted layouts, metadata coloring, search, zoom, ladderization, and SVG export.