Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Assembly and intrahost / low-frequency variant calling for viral samples

QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

Viral genome assemble and characterisation

Visualize microbial evolution at the SNP level!

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 reference guided assembler of highly variable viral genomes

bvas: bayesian viral allele selection

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.

Linked Multilocus Genotype by Sequencing (LMGSeq) applied to high-throughput quantification of genetic exchange among diverse human Influenza A virus strains

VIral GEnome ASsembly pipelines for WGS

Viral genome assembly pipeline for WGS using ONT

HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.

Detect Hepatitis A Virus Infection Clusters

UC Davis: Data Science for Biologists - R markdown