Virome Analysis Tools
Awesome-Virome contains a comprehensive collection of tools for various aspects of virome analysis. This page provides an overview of the tool categories and helps you navigate to the specific tools you need.
Tool Categories
The tools are organized into the following main categories:
| Category | Description | Key Tools |
|---|---|---|
| Virus and Phage Identification | Tools for identifying viral sequences in metagenomic data | VirSorter2, VIBRANT, geNomad |
| Host Prediction | Tools for predicting the bacterial hosts of phages | iPHoP, CHERRY, WIsH |
| Genome Analysis | Tools for assembling, annotating, and analyzing viral genomes | Pharokka, DRAMv, MetaProdigal |
| Taxonomy | Tools for taxonomic classification of viral sequences | vConTACT2, PhaGCN, VIPtree |
| Databases | Reference databases for viral sequences | NCBI RefSeq, ICTV VMR, pVOGs |
| Functional Analysis | Tools for functional annotation and analysis | BACPHLIP, PHACTS, PHROGs |
| Sequence Analysis | Tools for sequence alignment and translation | ViralMSA, pygenetic_code |
| Specialized Analysis | Tools for specific types of analysis | DeepVHPPI, vAMPirus, SpacePHARER |
Virus and Phage Identification
Tools for identifying viral sequences in metagenomic data:
Metagenome Analysis
- VirSorter2 - Random forest classifier for virus detection
- VIBRANT - Virus identification by combining boundary detection with annotation
- geNomad - Tool for identifying viral sequences, including proviruses
- DeepVirFinder - Neural network approach for viral contig identification
Integrated Viruses
- PhiSpy - Prophage identification combining similarity and composition-based approaches
- Phigaro - Prophage prediction tool
- viralintegration - Nextflow pipeline for detecting viral integration sites
RNA Virus Identification
- palmID - RNA virus RdRp search tool with R interface
- RdRp-scan - Search against the RdRp database
- metaviralSPAdes-RNA - RNA virus detection module
Host Prediction
Tools for predicting the bacterial hosts of phages:
- iPHoP - Integrated approach for phage host prediction
- CHERRY - Deep learning for phage host prediction
- VirHostMatcher-Net - Network-based virus-host prediction
- WIsH - Phage-host prediction using genome homology
Genome Analysis
Tools for assembling, annotating, and analyzing viral genomes:
Genome Annotation
- Pharokka - Rapid phage annotation tool
- DRAMv - Distilling and refining annotation of metabolism for phages
Genome Assembly
- metaviralSPAdes - Assembler for viruses from metagenomic data
- coronaSPAdes - HMM-synteny guided assembly for all viruses
Genome Completeness
- CheckV - Quality assessment for viral genomes
- viralComplete - Tool for checking viral genome completeness
Taxonomy
Tools for taxonomic classification of viral sequences:
- vConTACT2 - Viral taxonomy based on protein clusters
- PhaGCN - Graph convolutional network for phage taxonomy
- VIPtree - Viral proteomic tree-based classification
- ViPTree - Viral genome-based phylogenetic tree construction
Databases
Reference databases for viral sequences:
- NCBI Viral RefSeq - Reference viral genomes
- ICTV VMR - ICTV Virus Metadata Resource
- pVOGs - Prokaryotic Virus Orthologous Groups
- IMG/VR - Integrated database of viral sequences from metagenomes
- PhagesDB - Database of mycobacteriophage genomics
Functional Analysis
Tools for functional annotation and analysis:
- BACPHLIP - Bacteriophage lifestyle prediction
- PHACTS - Phage Classification Tool Set
- PHROGs - Phage Orthologous Groups annotation
- pVOGS - Database for virus orthologous groups
- PhageTerm - Phage termini and packaging identification
Sequence Analysis
Tools for sequence alignment and translation:
- ViralMSA - Reference-guided multiple sequence alignment for viral genomes
- pygenetic_code - Python package for genetic code manipulation
- VIGOR - Viral genome annotation
- VGAS - Viral genome annotation system
- VADR - Viral Annotation DefineR for sequence annotation
Specialized Analysis
Tools for specific types of analysis:
- DeepVHPPI - Prediction of virus-host protein-protein interactions
- vAMPirus - Processing viral amplicon data
- SpacePHARER - CRISPR-Cas target prediction
- HoloVir - Viral diversity in metagenomic datasets
- VirSorter - Mining viral signals from microbial genomes
Top Packages by Category
Here are the most starred packages in key categories:
Virus and Phage Identification
- BLAST+DIAMOND - ⭐ 1114 stars
- geNomad - ⭐ 219 stars
- VIBRANT - ⭐ 159 stars
Host Prediction
- CHERRY - ⭐ 24 stars
- VirHostMatcher-Net - ⭐ 21 stars
- DeepHost - ⭐ 17 stars
Genome Analysis
- metaviralSPAdes - ⭐ 797 stars
- Prodigal/MetaProdigal - ⭐ 471 stars
- Pharokka - ⭐ 158 stars
Tool Selection Guide
Not sure which tool to use? Check out our Selection Guide to find the right tools for your specific research needs.