Data preprocessing scripts and preprocessed data storage for COVID-19 Scenarios project

🍄 spora: Streamlined Phylogenomic Outbreak Report Analysis

Coronavirus genome analysis.

A Telegram bot to get the data of the COVID-19 (novel coronavirus) outbreak in Italy

ArcGIS Pro toolbox to extract and transform case and contact data from a Go.Data instance

A Discord bot created to track the COVID-19 outbreak

This geospatial project maps Marburg virus transmission, a zoonotic disease with high case fatality rates in Africa. It highlights the need for medical treatment, isolation, and quarantine measures. Vaccines and contact tracing can limit the global spread of epidemics

End to end workflow for CV-A24v: trimming, de novo assembly, reference mapping with masked consensus, MAFFT alignment, IQ-TREE phylogenies for whole genome and VP1, and amino acid comparison against D90457.1. Includes scripts to fetch context genomes and optional region slicing for recombination checks.

Reproducible workflow for RSV-A and RSV-B whole genome analysis that mirrors the Islamabad 2022 to 2023 study.

OUTBREAK! is a dashboard that automatically identifies potential outbreaks of CDC nationally notifiable diseases using weekly data and DeepAR forecasting on AWS.

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.

End to end Snakemake workflow for MuV genotype G. FastQC, Trimmomatic, Picard, SPAdes, BWA, masked consensus at depth 10, MAFFT, IQ-TREE with K2+I for SH and GTR+G for whole genome. Includes SH extraction, HN and F mutation tables, BLAST based context fetching, and full references with citation.