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

This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools

Data portal and API for Center for Viral Systems Biology (CViSB) data

VStrains is a de novo approach for reconstructing strains from viral quasispecies.

BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

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.

Viral genome assemble and characterisation

Set of tools for viral metagenomics.

Viral Metagenomics Assembly and Annotation Pipeline

This is a pipeline for exploring viruses (ssDNA, dsDNA phage, and giant DNA viruses) and viral diversity in metagenomes.

A streamlined Oxford Nanopore Viral Metagenomics Pipeline

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Viral genome coverage evaluation for metagenomic diagnostics 🩸

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

Detect iSNV and construct whole viral genomes from metagenomic samples