A comprehensive, curated database of 302+ software tools for virome analysis - the study of viral communities in various environments. This repository helps researchers navigate the complex landscape of tools for analyzing phages, viruses, and their interactions with hosts.

🎯 Perfect for:

• Researchers new to virome analysis seeking guidance
• Experienced scientists looking for specific tools
• Developers building viral analysis workflows
• Students learning computational virology

🚀 Key Features:

• Curated collection of 302+ tools across 8 major categories (including 10 new 2025 tools)
• Interactive dashboard with visualization and analytics
• Tool comparison matrix with filtering and export
• Automated metadata collection from GitHub/GitLab/Bitbucket
• RESTful API for programmatic access
• Weekly updates and quality assurance

Explore the full Awesome-Virome experience with our interactive web platform featuring:

• 📊 Interactive Dashboard - Visualize tool relationships, timelines, and trends
• 📖 Comprehensive Documentation - Learn virome analysis workflows step-by-step
• ⚖️ Tool Comparison - Compare tools side-by-side with advanced filtering
• 🧭 Selection Guide - Get personalized tool recommendations

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Don't just read about tools - explore them visually! Our interactive web applications make discovering and comparing viral analysis tools fast and intuitive.

Visualize the entire virome analysis ecosystem at a glance:

• Tool Categorization Treemap - See how 302+ tools are distributed across categories
• Interactive Network Graph - Explore relationships between tools and categories
• Timeline Visualization - Track the evolution of viral analysis tools over time
• Technology Trends - Analyze programming language usage across the collection

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Compare tools side-by-side to find the perfect fit:

• Multi-tool comparison with key metrics and features
• Advanced filtering by category, language, maintenance status
• Smart sorting by stars, update frequency, or custom criteria
• Export capabilities to CSV or JSON for further analysis

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Get personalized recommendations through our interactive decision tree:

• Answer simple questions about your research needs
• Follow guided pathways to narrow down options
• Receive tool recommendations tailored to your workflow
• Learn key features and requirements for each suggestion

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Virome analysis involves studying the collection of viruses (including bacteriophages) in a specific environment such as the human gut, soil, or oceans. These analyses typically include:

1. Identifying viral sequences in metagenomic data
2. Classifying viruses and predicting their hosts
3. Assembling and annotating viral genomes
4. Analyzing viral diversity and evolution
5. Studying virus-host interactions and functional potential

Note on Tool Availability: This list contains tools developed over many years. Some tools may no longer be actively maintained or might have moved to new locations. We mark tools that are no longer available as [unavailable] and provide archive links when possible. If you find a broken link or know of a tool's new location, please submit a PR or issue.

New to virome analysis? Here are the essential tools to get you started:

Basic Virome Analysis Workflow:

1. Quality control of metagenomic reads
2. Assembly of contigs (e.g., SPAdes, MEGAHIT)
3. Identification of viral contigs → Virus and Phage Identification
4. Quality assessment → Genome Analysis
5. Taxonomic classification → Taxonomy
6. Host prediction → Host Prediction
7. Functional annotation → Functional Analysis

🎯 Quick Access:

• Explore Interactive Tools ↑
• Browse All Tools by Category ↓

Here are the most popular and well-maintained tools in each major category:

📈 Most Starred Overall: 2. CovidMD (⭐ 2365) - Molecular dynamics for COVID-19

• What is Awesome-Virome?
• Explore Interactively
• Introduction to Virome Analysis
• Quick Start Guide
• Top Tools by Category

• Virus and Phage Identification
  • Metagenome Analysis
  • Integrated Viruses
  • RNA Virus Identification
• Host Prediction
• Genome Analysis
  • Genome Annotation
  • Genome Assembly
  • Genome Completeness
  • Genome Comparison
  • Gene Finding
• Taxonomy

• Databases
• Sequence Databases

• Functional Analysis
  • Evolutionary Analysis
  • Lifestyle Classification
  • Phage-specific Analysis
  • Viral Orthologous Groups
• Sequence Analysis
• CRISPR Analysis
• Other Tools

• API Support

• Contributing
• Repository Maintenance
• Acknowledgments
• License

• Cenote-Taker 2 [v2.1.5, 2022] - Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]
• Cenote-Taker 3 [v0.1.0, 2023] - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
• CoCoNet [Updated: 03/2025] - Neural networks for viral contig identification. [pip] [Python]
• crassus [Updated: 04/2023] - Snakemake workflow for phage discovery. [conda] [Python]
• DBSCAN-SWA [Updated: 12/2024] - DBSCAN clustering for phage identification. [Python]
• Deep6 [Updated: 03/2024] - Machine learning based virus identification. [Python]
• DeepVirFinder [Updated: 03/2025] - Neural network approach for viral contig identification. [Python]
• DePhT [Updated: 12/2024] - Deep-learning Phage Taxonomy for phage identification. [conda] [Python]
• FastViromeExplorer - Detects viral sequences and predicts abundance by pseudoalignment of reads to a database. [Java]
• GenomePeek - Taxonomic classification of multiple domains. [Python]
• hecatomb [Updated: 01/2025] - Pipeline for virus identification from metagenomic data. [Nextflow]
• HoloVir [Updated: 01/2024] - Pipeline for taxonomic classification and gene function assignment. [Perl]
• INHERIT [Updated: 03/2025] - BERT embedding-based phage identification. [Python]
• INSaFLU-TELEVIR [Updated: 01/2025] - Platform for virus identification and characterization. [Python]
• isling [Updated: 08/2021] - Split read alignment for virus identification. [Python]
• Jaeger [Updated: 03/2025] - Phage identification in metagenomes. [Python]
• Jovian [Updated: 01/2025] - Public health toolkit focused on human viruses. [Nextflow]
• LazyPipe - Taxonomic profiling and reference-based detection. [Nextflow]
• MARVEL [Updated: 02/2025] - Random forest classifier for phage identification (not for prophages). [Python]
• metaPhage - Pipeline for phage and virus identification. [conda] [Nextflow]
• MetaPhinder [Updated: 07/2024] - Integrates BLAST hits to multiple phage genomes to identify phage sequences. [Python]
• MetaPhlAn 4.1.0 [Updated: 03/2025] - Read mapping-based virus identification. [conda, pip] [Python]
• nf-core/viralmetagenome [v1.0.0, 2025] - Nextflow pipeline for viral genome reconstruction with iSNV detection from metagenomic samples. [Nextflow]
• PhaBox - Integrates several phage tools: PhaMer, PhaTYP, PhaGCN, and CHERRY. [conda] [Python]
• Phage tools [Updated: 01/2024] - Collection of tools for predicting and identifying phage in metagenomes. [Python]
• PHAMB [Updated: 02/2025] - Random forest based phage identification. [conda] [Python]
• phaMers [Updated: 04/2023] - K-mer and machine learning phage identification. [Python]
• Phanta [Updated: 03/2025] - K-mer read based classification via snakemake workflow. [yaml] [Python]
• PIGv [Updated: 12/2024] - Giant virus identification using Metabat binning, k-mer scoring, and marker genes. [source] [Python]
• PPR-Meta [Updated: 03/2025] - Convolutional neural network for phage prediction. [Python]
• Prophage Tracer - Split read alignment for prophage identification. [Python]
• Seeker [Updated: 08/2024] - LSTM-based phage identification (not recommended for prophages). [pip] [Python]
• Serratus - Website for virus discovery from public sequencing data. [cloud platform]
• VFM [Updated: 04/2023] - Virus finder in metagenomic data. [Python]
• VIBRANT [Updated: 02/2025] - Virus identification by combining boundary detection with annotation. [Python]
• VIGA [Updated: 10/2024] - Viral genome assembler. [pip] [Python]
• VIP [Updated: 08/2022] - Integrated pipeline for virus identification. [Python]
• ViralCC [Updated: 12/2024] - Viral sequence identification via machine learning. [Python]
• ViralConsensus [Updated: 12/2024] - Viral consensus sequence calling from sequencing data. [source] [Python]
• viralMetagenomicsPipeline [Updated: 11/2024] - Snakemake workflow combining virSorter and VirFinder. [Python]
• ViralWasm - WebAssembly tools for virus identification in the browser. [JavaScript]
• viraMiner [Updated: 12/2024] - CNN classifier for virus identification. [Python]
• virAnnot [Updated: 03/2024] - Pipeline for OTU assignment in viral sequences. [source] [Python]
• VirFinder [Updated: 03/2025] - Neural network and machine learning for virus identification. [R]
• Virhunter [Updated: 01/2025] - Deep learning approach for virus identification. [Python]
• VirMake [Updated: 02/2025] - Snakemake pipeline for viral taxonomic and functional analysis from shotgun metagenomic sequencing. [Snakemake] [Python]
• VirMine [Updated: 04/2023] - Pipeline for virus identification. [Perl]
• virMiner [Updated: 10/2024] - Random forest approach for virus identification. [R]
• VirNet [Updated: 09/2024] - Neural network for phage identification. [Python]
• ViroProfiler [Updated: 02/2025] - Comprehensive phage profiling pipeline. [Nextflow]
• VirSorter [Updated: 01/2025] - Detection of viral sequences from microbial genomic data. [bioconda] [Perl] [legacy]
• VirSorter2 [v2.2.4, 2023] - Random forest classifier for virus detection. [conda] [Python] [v2.2.4, 2023]
• Virtifier [Updated: 11/2024] - LSTM neural network for virus identification. [Python]
• Virtus [Updated: 10/2024] - Virus sequence detection workflow. [Snakemake]
• virus_prediction [unavailable] - Nextflow pipeline with virSorter. [Nextflow]
• ViruSpy [Updated: 11/2024] - Virus detection pipeline. [Python]
• VirusSeeker - Pipeline for virus detection from sequence data. [source] [Perl]
• vRhyme [Updated: 02/2025] - Machine learning for viral binning from metagenomes. [conda] [Python]
• What_the_phage [Updated: 02/2025] - Nextflow workflow combining multiple phage identification tools. [Nextflow]

• DRAD - Dinucleotide Relative Abundance difference method (no longer available).
• geNomad [v1.6.0, 2023] [v1.6.0, 2023] [Updated: 03/2025] - Tool for identifying viral sequences, including proviruses. [conda] [Python] [v1.6.0, 2023]
• hafeZ [Updated: 08/2024] - Readmapping approach for integrated phage identification. [Python]
• LysoPhD - Phage identification tool (code not available).
• phage_finder - Pipeline for prophage identification. [Perl] [legacy]
• phageboost - Machine learning with boost algorithm for prophage detection. [R]
• PhageWeb - Web server for phage identification (API available). [web service]
• PHASTER - Rapid identification and annotation of prophage sequences (web service only). [web service]
• Phigaro [Updated: 12/2024] - Prophage prediction tool. (Note: downloads uncompressed file from Russian server). [Python]
• PhiSpy [v4.2.23, 2023] - Prophage identification combining similarity and composition-based approaches. [conda, pip] [Python] [v4.2.23, 2023]
• PIDE [Updated: 02/2025] - Prophage island detection using ESM-2 protein language model and gene density clustering. [Python]
• Prophet [Updated: 12/2023] - Prophage prediction tool. (Note: requires unsupported legacy software). [Perl] [legacy]
• Prophinder - Web-based prophage detection tool. [web service]
• VAPiD [Updated: 09/2024] - Virus genome annotation and identification tool. [pip] [Python]
• viralintegration [Updated: 12/2024] - Nextflow pipeline for detecting viral integration sites. [conda] [Nextflow]

• palmID - RNA virus RdRp search tool with R interface. [source, R] [R]
• RdRp-scan [Updated: 07/2024] - Search against the RdRp database. [source] [Python]
• rdrpsearch - Iterative HMM search of viral RdRp to detect distant homologs. [source] [Python]
• RNA-Virus-Flow [unavailable] - Pipeline for RNA virus assembly and analysis. [Nextflow]

• BacteriophageHostPrediction [Updated: 01/2025] - Computational methods for phage-host prediction. [Python]
• CHERRY [v1.0, 2022] [v1.0, 2022] [Updated: 03/2025] - Deep learning for phage host prediction. [Python] [v1.0, 2022]
• CrisprOpenDB [Updated: 07/2024] - 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 [Updated: 01/2025] - CNN for phage host prediction. [Python]
• HostG [v1.0, 2022] - Graph convolutional network for phage host prediction. [Python] [v1.0, 2022]
• HostPhinder [Updated: 11/2024] - K-mer based phage host prediction. [Python]
• INFH-VH [Updated: 11/2024] - Integrating different features for virus-host prediction. [Python]
• iPHoP [v1.3.3, 2023] - Integrated approach for phage host prediction. Documentation at https://bitbucket.org/srouxjgi/iphop/src/main/ [v1.3.3, 2023]. [bioconda] [Python] [v1.3.3, 2023]
• MVP [unavailable] - Microbe-virus database with prediction tools. [web service]
• PB-LKS [Updated: 02/2025] - K-mer profiles for phage-bacteria prediction. [Python]
• PhageHostLearn [Updated: 02/2025] - Machine learning for phage-host prediction. [Python]
• PhageRBPdetect - HMMs & machine learning for receptor-binding protein detection. [Python]
• PHERI [Updated: 10/2022] - Phage-host interaction prediction tool. [Python]
• PHIAF [Updated: 10/2024] - GAN-based phage-host interaction prediction. [Python]
• PHISDetector - Phage-host interaction detection. [web service]
• PHIST [Updated: 01/2025] - K-mer based phage-host prediction. [source] [C++]
• PHP [Updated: 11/2024] - Phage host prediction tool. [Python]
• PHPGCA [Updated: 11/2024] - Similarity graphs for phage-host prediction. [Python]
• PredPHI [Updated: 10/2024] - Phage-host interaction prediction. [Python]
• RaFaH - Random Forest approach for phage host prediction. [Python]
• vHulk - Virus host prediction tool. [Python]
• VIDHOP [Updated: 03/2025] - Deep learning for virus-host prediction. [conda] [Python]
• VirHostMatcher [Updated: 01/2025] - Oligonucleotide frequency-based host prediction. [Python]
• VirHostMatcher-Net [Updated: 09/2024] - Network-based virus-host prediction. [Python]
• VirMatcher [v1.0, 2022] - Multiple methods for phage host prediction with confidence scores. [conda] [Python] [v1.0, 2022]
• Virus Host DB - Database for virus-host relationships. [web service]
• Virus Host Predict [Updated: 05/2024] - Host prediction for viral sequences. [Python]
• WIsH [Updated: 10/2024] - Phage-host prediction using genome homology. [C++]

• DRAMv [v1.4.6, 2023] - Distilling and refining annotation of metabolism for phages. [conda, pip] [Python] [v1.4.6, 2023]
• MetaCerberus [Updated: 03/2025] - HMM-based annotation with Ray MPP. [conda, pip] [Python]
• PhANNs [Updated: 12/2024] - Phage annotation neural networks. (Python version available via contact) [Python]
• Pharokka [v1.5.0, 2023] [v1.5.0, 2023] [Updated: 03/2025] - Rapid phage annotation tool. [conda] [Python] [v1.5.0, 2023]
• Phold [v1.1.0, 2025] - Phage annotation using protein structure information with ProstT5 and Foldseek. [conda, pip] [Python]

• BonoboFlow [v1.0, 2025] - Nextflow pipeline for viral genome assembly and haplotype reconstruction from ONT long reads. [Nextflow] [Python]
• coronaSPAdes [Updated: 03/2025] - HMM-synteny guided assembly for all viruses. [C++]
• metaviralSPAdes [Updated: 03/2025] - Assembler for viruses from metagenomic data. [C++]
• VEGA [Updated: 03/2025] - Snakemake workflow for viral genome assembly. [conda] [Snakemake]

• CheckV [v1.0.1, 2022] - Quality assessment for viral genomes. (Not recommended for prophages) [conda, pip] [Python] [v1.0.1, 2022]
• viralComplete [Updated: 11/2024] - Tool for checking viral genome completeness. [Python]
• viralVerify [Updated: 01/2025] - Verification of viral contigs. [Python]

• mulitPHATE [Updated: 10/2022] - Multi-phage annotation and comparison tool. [Python]
• PhageClouds - Network graphs for phage comparison (website down, source code not found).

• GeneMarkS - Gene prediction tool with specific models for viral sequences. [web service] [Perl/C++]
• GeneMarkS-2 - Improved version of GeneMarkS with enhanced performance for phage genomes. [web service] [Perl/C++]
• PHANOTATE [Updated: 01/2025] - Phage gene finder using a graph-based algorithm to identify ORFs missed by other programs. [Python]
• PhageBoost [Updated: 02/2025] - Machine learning tool for identifying structural proteins in phage genomes. [R]
• PhiSpy [v4.2.23, 2023] - While primarily for prophage identification, includes ORF prediction capabilities. [conda, pip] [Python]
• VIGOR [unavailable] - Viral genome annotation tool designed specifically for viral genomes, primarily eukaryotic viruses. [source] [Java/Perl]
• PhageTerm - Tool for identifying phage termini and packaging mechanisms, helpful for ORF identification. [source] [Python]
• Pharokka [v1.5.0, 2023] [v1.5.0, 2023] [Updated: 03/2025] - Dedicated phage annotation tool that includes ORF prediction. [conda] [Python]
• VGAS [unavailable] - Comprehensive pipeline for viral genome annotation including gene finding. [source] [Python]

• Sphae [Updated: 03/2025] - Phage toolkit to assemble and annotate phages, to identify phage therapy candidates [conda] [Snakemake]

• BERTax [Updated: 02/2025] - BERT-based viral taxonomy tool. [Python]
• Classiphages 2.0 - Artificial neural network for phage classification (code not available).
• GraViTy [Updated: 12/2024] - HMMs and genome organization models for virus taxonomy. [R]
• PhaGCN [v1.0, 2022] [v1.0, 2022] [Updated: 02/2025] - Graph convolutional network for phage taxonomy. [Python] [v1.0, 2022]
• vConTACT [Updated: 10/2016] - Whole-genome gene-sharing networks for virus taxonomy. [Python] [legacy]
• vConTACT2.0 [v0.9.19, 2023] [v0.9.19, 2023] [Updated: 11/2022] - Updated version of vConTACT with improved performance. [Python] [v0.9.19, 2023]
• VICTOR - Genome-based phylogeny and classification of phages. [web service]
• VIPtree [Updated: 02/2025] - Viral proteomic tree generation tool. [Perl]
• VIRIDIC - Virus intergenomic distance calculator. [R]
• VIRify [Updated: 03/2025] - Nextflow pipeline for viral taxonomy. [Nextflow]
• VirusTaxo [Updated: 01/2024] - K-mer enrichment method for viral taxonomy. [source] [Python]
• VPF Tools [Updated: 01/2025] - Viral protein family analysis tools. [Python]

• FDA ARGOS - Curated database of reference genomes of microbial sequences, for diagnostic use. [web service] [Updated 2023]
• ICTV Virus Metadata Resource (VMR) - Curated database of sequences of exemplars for each classified virus species. [Updated 2023]
• NCBI RefSeq - Curated database of annotated genomic, transcript, and protein sequence records: viruses (ca. 8500 complete viral genomes), prokaryotes, eukaryotes. [Updated 2023]
• NCBI GenBank - Uncurated database of all publicly available nucleotide sequences, annotated. [Updated 2023]
• Reference Viral DataBase (RVDB), nucleic version - Curated database of virus nucleotide sequences, available as Unclustered (U-) and Clustered (C-) nucleotide sequence files. [Updated 2023]
• Reference Viral DataBase (RVDB), protein version - Protein version (RVDB-prot and RVDB-prot-HMM) of the curated U-RVDB described above. [Updated 2023]
• SIB Viral reference sequences - Curated database of annotated viral genomes generated by the Swiss Institute of Bioinformatics (SIB). [Updated 2023]
• UniProt Virus proteomes - Curated and annotated database of proteomic virus references (ca. 10,000 virus reference proteomes). [Updated 2023]
• VirMet [Updated: 11/2024] - In-house database download from GenBank of viral references. [Python]
• Virosaurus - Curated database of virus sequences for clinical metagenomics, clustered (non-redundant). [Updated 2022]
• Virus Pathogen Resource (ViPR) - Curated database of virus pathogens (ca. 1,000,000 genomes from ca. 7000 species). [web service] [Updated 2023]
• Virion [Updated: 02/2025] - An open database of vertebrate-virus interactions. [R]

• CHVD - Comprehensive human virus database. [2021]
• Earth Virome - Collection of viral sequences from environmental samples. [2021]
• GOV-RNA - Global Ocean RNA viruses sequence database. [2021]
• GOV2.0 - Global Ocean DNA viruses sequence database. [2021]
• GPDB - Gut phage database. [2021]
• GVD - Global virome database. [2020]
• KEGG Virus - KEGG collection of virus genomes. [Updated 2023]
• mMGE - Mobile genetic element database. [Updated 2023]
• PhagesDB - Database of phage genomes. [Updated 2023]
• ViromeDB - Public collection of >162,000 viral sequences. [2019]
• Viruses.String - Virus-host protein-protein interactions database. [Updated 2022]

• OLGenie [Updated: 10/2024] - Program for estimating dN/dS in overlapping genes. [source, Perl] [Perl]
• SNPGenie [Updated: 02/2025] - Program for estimating πN/πS and diversity measures. [conda, Perl] [Perl]
• VCFgenie [Updated: 09/2024] - Program for filtering VCF files and eliminating false positive variants. [source, Python] [Python]
• VIPERA [Updated: 03/2025] - Phylogenetic and population genetics analysis of intra-patient SARS-CoV-2. [source] [R]

• BACPHLIP [v0.9.6, 2023] - Random Forest classifier for phage lifestyle. [conda, pip] [Python] [v0.9.6, 2023]
• PHACTS [Updated: 03/2025] - Phage classification tool suite. [Python]
• PhageAI - NLP, ML for phage lifestyle classification. [pip] [Python]

• Phanotate [Updated: 01/2025] - Phage gene finder. [Python]
• PHROGs - Phage-specific orthologous groups. [Database, 2021]
• PHRED - Phage receptor identification tool (no longer available).
• SpikeHunter [Updated: 01/2025] - Phage tail spike identification using protein embeddings. [Python]

• efam - Expanded metaproteome-supported HMM profile database of viral protein families. [2020]
• pVOGs - Prokaryotic virus orthologous groups. [Database]
• VogDB - Virus orthologous groups database. [Database, Updated 2023]

• MaGplotR [Updated: 11/2024] - CRISPR screen visualization tool. [R]
• SpacePHARER [Updated: 11/2024] - CRISPR spacer phage-host pair finder. [C++]

• ViralMSA [Updated: 01/2025] - Python script for viral multiple sequence alignment using read mappers. [source] [Python]

• pygenetic_code [Updated: 04/2024] - C and Python tools for genetic code translation. [conda, pip] [Python]

• BVBRC - BV-BRC website for virus bioinformatics. [web service]
• iVirus 2.0 - Integrated iVirus apps on CyVerse and KBase. [web service]

• PlaqueSizeTool [Updated: 07/2024] - Computer vision tool for measuring phage plaques. [pip] [Python]
• PlaqueSizeTool (colab) - Google Colab version of PlaqueSizeTool. [web service]

• FAVITES [Updated: 08/2024] - Simulate contact networks, transmission, phylogenies, and sequences. [source] [Python]
• FAVITES-Lite [Updated: 02/2025] - Lighter version of FAVITES. [source] [Python]

• ViromeQC [Updated: 10/2024] - Virome quality control and contamination assessment. [source] [Python]

• vAMPirus [Updated: 05/2024] - Nextflow pipeline for virus amplicon processing and analysis. [conda] [Nextflow]

• COBRA [Updated: 02/2025] - Viral strain reconstruction using contig overlaps. [Python]
• Phables [Updated: 01/2025] - Flow decomposition on assembly graphs for phage strain reconstruction. [conda, pip] [Python]
• VStrains [Updated: 11/2024] - Viral strain reconstruction from metagenomic data. [Python]

• TrIdent - Transduction identification via read coverage pattern matching. [R]

• DeepVHPPI [Updated: 12/2024] - Deep learning for virus-host protein-protein interactions. [Python]
• DePP [unavailable] - Depolymerase finder for phages. [web service]
• PhageDPO - SVM and ANN for phage depolymerase prediction. [Python]
• PhageTB [Updated: 11/2024] - BLAST-based phage therapy tools. [Python]
• PhageTerm - Predicting phage packaging mechanism. [source] [Python]
• PhagePromoter [Updated: 02/2025] - ANN, SVM for phage promoter prediction. [source] [Python]
• VIRMOTIF - Tool for identifying viral genome motifs. [Python]

• VIPERdb - Virus particle explorer database with structure visualization. [web service]
• VIRALpro - Viral capsid and tail protein prediction. [web service]

• PHANOTATE-AMR [Updated: 01/2025] - Extension adding AMR gene identification in phages. [Python]
• VirAMR [unavailable] - Detects antimicrobial resistance genes in viral genomes. [Python]

• metaviralSPAdes-RNA [Updated: 03/2025] - RNA virus detection module. [C++]
• VirMine-RNA [Updated: 04/2023] - Focused on detecting RNA viruses in transcriptomic data. [Python]
• VirusTAP [unavailable] - Transcriptome Assembler Pipeline for viral sequence discovery. [Perl]

• CliqueSNV [Updated: 12/2024] - Reconstruction of virus haplotypes in a mixed population. [Java]
• QuRe - Viral quasispecies reconstruction tool. [Java]
• ShoRAH [Updated: 12/2024] - Short reads assembly into haplotypes for viral population. [C++]
• V-pipe [Updated: 03/2025] - Pipeline for viral population analysis. [Nextflow]
• ViQuaS [unavailable] - Viral Quasispecies reconstruction. [Python]

• CloVR-Microbe [unavailable] - Cloud-based viral metagenomics pipeline. [Perl]
• IDseq [Updated: 03/2025] - Pathogen detection platform with viral analysis components. [Ruby]
• Viral Beacon [unavailable] - Cloud platform for virus sequence sharing and analysis. [Python]
• Viral-NGS [Updated: 02/2025] - Broad Institute's viral genomic analysis on cloud. [Python]

• CHERRY-models [Updated: 03/2025] - Pre-trained host prediction models. [Python]
• DeepVirFinder-models [Updated: 03/2025] - Pre-trained models for viral sequence identification. [Python]
• PhaTYP-models [unavailable] - Phage lifestyle prediction models. [Python]
• ViraMiner-models [Updated: 12/2024] - ML models for viral sequence mining. [Python]

• MAVERIC [unavailable] - Analyzing viral infections at the single-cell level. [Python]
• scViroCap [unavailable] - Single-cell viral capture sequencing analysis. [Python]
• scVIRseq [unavailable] - Single-cell virus infection profiling. [Python]
• Viral-Track [Updated: 12/2024] - Tracking viruses in single-cell RNA-Seq data. [R]

• GlycoProtViz [unavailable] - Visualizing viral glycoprotein structures. [Python]
• GlyConnect - Database with viral glycosylation data. [web service]
• NetNGlyc - N-glycosylation site prediction in viral proteins. [web service]
• pGlyco [Updated: 02/2025] - Glycopeptide identification in viral proteins. [C++]

• EVE [unavailable] - Ancient viral element detection in genomes. [Python]
• HOPS [Updated: 10/2024] - Pathogen screening for ancient DNA, includes viral sequences. [Java]
• Paleovirology [Updated: 10/2024] - Tools for detecting ancient viral elements. [Perl]
• PastML [Updated: 01/2025] - Useful for ancient viral sequence reconstruction. [Python]

• EpiDOCK - Viral epitope docking and analysis. [web service]
• IEDB-tools [unavailable] - Suite of tools for epitope prediction. [Python]
• NetMHCpan - Neural network for MHC binding prediction in viral proteins. [web service]
• TepiTool - T-cell epitope prediction for viral sequences. [web service]

• CHARMM-GUI - Web-based interface for viral particle simulation setup. [web service]
• CovidMD [Updated: 03/2025] - COVID-19 specific molecular dynamics toolbox (extensible to other viruses). [C++]
• NAMD-VIRAL - Molecular dynamics simulations of viral proteins. [C++]
• VMD-Viral - Visualization of viral molecular dynamics. [C++]

• DarkVirome [unavailable] - Analysis of unclassified viral sequences. [Python]
• Recentrifuge [Updated: 02/2025] - Classification tool for novel sequences. [Python]
• VirSorter-DarkMatter [Updated: 01/2025] - Extension focused on novel viral sequences. [Perl]

Please feel free to contribute!

This repository welcomes contributions from the community. Here's how you can help:

1. Add New Tools: Submit entries for tools not yet included in the list
2. Update Information: Help keep tool descriptions and links up to date
3. Report Issues: Let us know about broken links or outdated information
4. Improve Documentation: Suggest enhancements to the documentation
5. Fix Bugs: Help resolve issues with the website or dashboard

We provide standardized issue templates to make contributing easier:

• Tool Addition: Template for suggesting new tools
• Tool Update: Template for updating existing tool information
• Bug Report: Template for reporting issues with the repository
• Feature Request: Template for suggesting new features

For more details, see our contribution guidelines.

This repository uses a streamlined GitHub Actions workflow system to maintain data and deployments:

1. Automated Updates: Weekly basic updates and monthly comprehensive metadata updates
2. Data Management: All data is stored in data.json and displayed through GitHub Pages
3. Contribution Flow: External contributors can propose changes via Pull Requests
4. API Access: Programmatic access to the database via a REST API
5. Automated Changelog: Monthly release notes documenting tool additions, updates, and removals

For technical details, see the workflow documentation and view our release notes.

This repository features an enhanced metadata collection system that enriches tool information with details from GitHub, GitLab, and Bitbucket repositories:

• Repository Statistics: Star counts, forks, open issues, and watchers
• License Information: License type and details for each tool
• Programming Languages: Primary and secondary languages used
• Repository Topics/Tags: Topic classifications from repository metadata
• Release Information: Latest release version and date
• Creation & Update Dates: When repositories were created and last updated

This metadata is updated monthly and integrated into our visualization and search capabilities, making it easier to discover tools based on popularity, language preferences, or specific features.

This list was originally started by Rob Edwards and his team at Flinders University and would not have been possible without their original hard work and dedication.

Awesome-Virome provides a REST API that allows programmatic access to the curated database of virome analysis tools. This enables developers and researchers to build applications, workflows, or custom analyses on top of the dataset.

• Base URL: https://shandley.github.io/awesome-virome/api/v1/
• Format: All endpoints return JSON
• Authentication: No authentication required
• CORS-Enabled: Accessible from browser applications

• All Tools: /api/v1/tools.json - Complete list of all tools with metadata
• Categories: /api/v1/categories.json - List of all tool categories
• Search Index: /api/v1/search.json - Lightweight index for client-side filtering
• Statistics: /api/v1/stats.json - Aggregate statistics about the tools collection
• Category-Specific: /api/v1/categories/{category_slug}.json - Tools filtered by category

The API can be used with standard HTTP requests in any programming language:

// JavaScript example
fetch('https://shandley.github.io/awesome-virome/api/v1/tools.json')
  .then(response => response.json())
  .then(data => {
    console.log(`Found ${data.count} tools`);
    // Use the data for visualization, filtering, etc.
  });

For complete documentation and additional examples in Python and R, see the API documentation.

Awesome-Virome offers several unique features that enhance its value as a resource for the viral bioinformatics community:

• Dynamic network graph showing tool relationships and connections
• Tool categorization treemap for understanding the ecosystem
• Timeline visualization showing field development over time

• Automated metadata enrichment from GitHub, GitLab and Bitbucket
• Detailed repository statistics including stars, forks, and languages
• License information and release history tracking
• Programming language distribution analysis

• Standardized issue templates for tool additions and updates
• Automated workflows for data validation and site health checks
• Detailed contribution guidelines for consistent data entry
• Regular updates to ensure tool information remains current

• Web interface for browsing and searching tools
• Interactive dashboard for visual exploration
• RESTful API for programmatic access
• Markdown files for simple text-based access

This repository includes a Python script (update_check.py) that automatically checks when each GitHub, GitLab, and Bitbucket repository was last updated. To use it:

1. Clone this repository
2. Install required packages: pip install requests
3. Set your GitHub API token (optional, but recommended to avoid rate limits):

   export GITHUB_TOKEN=your_github_token
   

4. Run the script:

   python update_check.py
   

The script will:

• Check all repository URLs in the README
• Fetch the last update time for each repository
• Update the README with [Updated: MM/YYYY] tags
• Mark unavailable repositories with [unavailable]
• Generate an unavailable_repos.md file listing all repositories that returned 404 errors
• Save all results to repo_updates.json for future reference

For better results, run this script periodically to keep the list current.

This README was last updated on May 3, 2025.