awesome-virome
github.com/shandley/awesome-virome ↗A listing of software, tools and databases useful for virome analysis
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me lifestyle classification resources from awesome-virome"
Installation instructions →What's inside
Functional Analysis
- BACPHLIPLifestyle Classification
Random Forest classifier for phage lifestyle. [conda, pip] [Python] [v0.9.6, 2023]
- efamViral Orthologous Groups
Expanded metaproteome-supported HMM profile database of viral protein families. [2020]
- OLGenieEvolutionary Analysis
Program for estimating dN/dS in overlapping genes. [source, Perl] [Perl]
- PHACTSLifestyle Classification
Phage classification tool suite. [Python]
- PhageAILifestyle Classification
NLP, ML for phage lifestyle classification. [pip] [Python]
- PHREDPhage-specific Analysis
Phage receptor identification tool (no longer available).
Host Prediction
- BacteriophageHostPrediction
Computational methods for phage-host prediction. [Python]
- CrisprOpenDB
CRISPR spacer database for phage-host prediction. [Python]
- DeePaC
CNN, ResNet for detection of novel human pathogens. [conda, pip] [Python]
- DeePaC-Live
DeePaC plugin for real-time analysis during sequencing. [conda, pip] [Python]
- DeepHost
CNN for phage host prediction. [Python]
- HostG
Graph convolutional network for phage host prediction. [Python] [v1.0, 2022]
Taxonomy
- BERTax
BERT-based viral taxonomy tool. [Python]
- Classiphages 2.0
Artificial neural network for phage classification (code not available).
- GraViTy
HMMs and genome organization models for virus taxonomy. [R]
- PhaGCN
Graph convolutional network for phage taxonomy. [Python] [v1.0, 2022]
- vConTACT
Whole-genome gene-sharing networks for virus taxonomy. [Python] [legacy]
- vConTACT2.0
Updated version of vConTACT with improved performance. [Python] [v0.9.19, 2023]
Genome Analysis
- BonoboFlowGenome Assembly
Nextflow pipeline for viral genome assembly and haplotype reconstruction from ONT long reads. [Nextflow] [Python]
- CheckVGenome Completeness
Quality assessment for viral genomes. (Not recommended for prophages) [conda, pip] [Python] [v1.0.1, 2022]
- DRAMvGenome Annotation
Distilling and refining annotation of metabolism for phages. [conda, pip] [Python] [v1.4.6, 2023]
- GeneMarkSGene Finding
Gene prediction tool with specific models for viral sequences. [web service] [Perl/C++]
- GeneMarkS-2Gene Finding
Improved version of GeneMarkS with enhanced performance for phage genomes. [web service] [Perl/C++]
- MetaCerberusGenome Annotation
HMM-based annotation with Ray MPP. [conda, pip] [Python]
Visualization and Infrastructure
- BVBRCCyberinfrastructure
BV-BRC website for virus bioinformatics. [web service]
- iVirus 2.0Cyberinfrastructure
Integrated iVirus apps on CyVerse and KBase. [web service]
- PlaqueSizeToolPlaque Analysis
Computer vision tool for measuring phage plaques. [pip] [Python]
- PlaqueSizeTool (colab)Plaque Analysis
Google Colab version of PlaqueSizeTool. [web service]
Virus and Phage Identification
- Cenote-Taker 2Metagenome Analysis
Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]
- Cenote-Taker 3Metagenome Analysis
Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
- CoCoNetMetagenome Analysis
Neural networks for viral contig identification. [pip] [Python]
- crassusMetagenome Analysis
Snakemake workflow for phage discovery. [conda] [Python]
- DBSCAN-SWAMetagenome Analysis
DBSCAN clustering for phage identification. [Python]
- Deep6Metagenome Analysis
Machine learning based virus identification. [Python]
Other Tools
- CHERRY-modelsMachine Learning Models
Pre-trained host prediction models. [Python]
- CliqueSNVViral Quasispecies Analysis
Reconstruction of virus haplotypes in a mixed population. [Java]
- CloVR-MicrobeCloud-based Viral Analysis
Cloud-based viral metagenomics pipeline. [Perl]
- COBRAViral Strain Reconstruction
Viral strain reconstruction using contig overlaps. [Python]
- DarkViromeDark Matter Viral Analysis
Analysis of unclassified viral sequences. [Python]
- DeepVHPPIInteraction Analysis
Deep learning for virus-host protein-protein interactions. [Python]
Sequence Databases
Showing a sample of 243 resources. View the full list on GitHub →