Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

FluMut is a command-line tool to find markers of interest in H5N1 avian influenza viruses.

genetic distance plotting for recombination events analysis

ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

The art of decorating a phage genome by gluing feature cutouts into it.

TrueConsense is a consensus caller for viral-targets that create biologically correct consensus sequences. TrueConsense keeps track of open reading frames, compensates for common sequencing or alignment artefacts, and is able to generate consensus sequences on multiple coverage-thresholds at the same time

NGS data analysis scripts for HBV elimination research group

Fitness estimates of SARS-CoV-2 variants

A bioinformatics tool for detecting defects in HIV-1 proviral sequences.

Git-based viral taxonomy management system - track changes, migrate datasets, and cite specific versions. Website: https://shandley.github.io/ICTV-git/

NGS data analysis scripts for HBV elimination research group

glimmer - genetics information gathering CLI tool.

An influenza virus model examining the effects of cellular regeneration on cell-to-cell and cell-free viral transmission.

Master cutting-edge genomics and bioinformatics approaches to advance viral diagnostics and investigation

BioVoice: virology Skill for the FluBroad Agent Framework — influenza bnAb research, universal vaccine literature, structural immunology

Code base for analyzing H5N1 (2.3.4.4b) adaptation via NA stalk-length and HA glycosylation-site variation, with reproducible pipelines for data parsing and visualization (bubble / 3D KDE).

Interactive agent-based epidemic simulator built with Dash and NumPy. Supports real-world and fictional disease presets, quarantine modeling, and live SEIRD curve tracking.

Advanced epidemiological framework integrating stochastic SEIRD models, Bortman endemic channels, wastewater biosecurity tracking, and ERA5 climate correlations. Engineered to anticipate zoonotic spillovers and monitor global nucleotide diversity in real time.