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

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

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

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

Scripts and data for the CoVaRR-Net Pillar 6 notebook

Automated genomic analysis of SARS-CoV-2 sequence data

Cluster Investigation & Virus Epidemiology Tool

Complete pipeline that mirrors the manuscript: reference based assembly with depth masking, de novo checks, phylogeny with configurable models including ModelFinder, and targeted mutation analysis for G and F versus NC_038235.1 and NC_001781.1. Includes CI and environment files for easy setup.

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."

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.

Tutorial for Polygenic Risk Score development

Gallery for GEViT Project

Dr. Buqing Yi