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

A GLUE project for Rabies Virus (RABV).

Scripts and data for the CoVaRR-Net Pillar 6 notebook

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

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."

Automated genomic analysis of SARS-CoV-2 sequence data

Cluster Investigation & Virus Epidemiology Tool

SNP-based phylogenomics workflow for bacterial genomes integrating Snippy, Gubbins, and IQ-TREE2 for variant calling, recombination filtering, and maximum-likelihood tree inference.

End to end Snakemake workflow for DENV-1 and DENV-2. FastQC, Trimmomatic, Picard, SPAdes, BWA, bcftools masked consensus at depth 10, MAFFT, IQ-TREE with GTR+G+I, BLAST driven context fetching, polyprotein translation and mutation tables. Includes full references and citation.

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.