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

A genome diagram generator for microbes and organelles

Viral (meta)-genome assembly pipeline.

Visualize microbial evolution at the SNP level!

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

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

QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

Pipeline for creating comprehensive viral reference sets.

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.

Viral genome assemble and characterisation

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.

VIral GEnome ASsembly pipelines for WGS

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.

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.

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

Viral genome assembly pipeline for WGS using ONT

A bioinformatics tool for designing primers and generating consensus sequences in viral genome analysis. It supports processing multiple aligned genomic sequences, optimizing primers, and visualizing genome annotations.

UC Davis: Data Science for Biologists - R markdown

Detect Hepatitis A Virus Infection Clusters

Uses k-means prediction to ascertain genomic sequences within ambiguously attributed fasta format data. The resulting cluster sequences are used to develop NCBI BLAST requests.

A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing

Hunting for CMV and HHV-6 in cfDNA sequence

Kamal_Acharya

RecombinHunt (alias for the software contained in this repository) is a Python library implementing a data-driven novel method for identifying contributing lineages and breakpoints in recombinant viral sequences.

Repository for analyses of HHV-6 reactivation using genomics