Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Reference-based consensus creation
Viral (meta)-genome assembly pipeline.
Visualize microbial evolution at the SNP level!
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8
Assembly and intrahost / low-frequency variant calling for viral samples
Pipeline for creating comprehensive viral reference sets.
QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture
This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.
A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.
Viral genome assemble and characterisation
A reference guided assembler of highly variable viral genomes
bvas: bayesian viral allele selection
Codebase for: Forecasting viral evolution from phylogenetic trees (Specht et al., 2026)
VIral GEnome ASsembly pipelines for WGS
a set of tools for viral amplicon schemes
Reference-based alignment and sequence database search of SARS-CoV-2 genomes.
Data portal and API for Center for Viral Systems Biology (CViSB) data
High accuracy single molecule Nanopore reads using the MrHAMER pipeline
TopONE is a project that studies recombination events using topological data analysis. This was made in the PGC-BTIP 2024 internship by Alfonso Miguel Cruz and Claire Angelie Gabisay, and mentored by C.J. Palpal-latoc.
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