Compare · 6 tools
Phage and virus genomics tools you can run online
Computational pipelines and classifiers for detecting viral and phage sequences, estimating assembly completeness, annotating phage genes, and classifying phage lifestyles and taxonomy.
What phage and virus genomics tools do
Viral and bacteriophage genomics involves discovering, evaluating, and interpreting viral sequences derived from isolates, metagenomes, or transcriptomes. Because viral genomes exhibit high divergence, compact gene organisation, and mosaic architecture, standard bacterial or eukaryotic genomic workflows are often insufficient. Dedicated tools identify viral and plasmid contigs within mixed sequencing data, delineate proviral boundaries within host chromosomes, assess sequence completeness and contamination, and assign taxonomy or biological traits such as infection lifestyle.
The approaches employed across this category combine profile hidden Markov models (HMMs), reference alignment algorithms, and machine learning architectures. Some tools deploy neural networks alongside protein marker databases to distinguish mobile elements from host sequences, whilst others employ profile HMMs to pinpoint specific conserved enzymes—such as RNA-dependent RNA polymerases or temperate-associated domains—or quantify genome completeness against curated reference databases.
Compared
- geNomadPhage and virus biologyIdentifies plasmids and viruses in sequencing data, predicts proviruses, and assigns viral taxonomy.See its pageAs a job
- CheckVPhage and virus biologyA command-line pipeline for assessing the completeness, contamination, and quality of viral genomes from metagenomes.See its pageAs a job
- PharokkaPhage and virus biologyRapid, standardised genome annotation pipeline for bacteriophage isolates and metaviromes.See its pageAs a job
- BACPHLIPPhage and virus biologyPredicts whether a bacteriophage genome represents a temperate or virulent lifestyle using conserved protein domains.See its pageAs a job
- taxmyPHAGEPhage and virus biologyClassifies complete dsDNA bacteriophage genomes to genus and species following official ICTV guidelines.See its pageAs a job
- RdRpCATCHPhage and virus biologyIdentifies RNA virus RNA-dependent RNA polymerase sequences using aggregated profile hidden Markov models.See its pageAs a job
How to choose
When screening uncharacterised sequencing datasets, geNomad identifies plasmids, viruses, and integrated proviruses across isolates, metagenomes, and metatranscriptomes using a hybrid neural network and marker framework. For targeted RNA virus discovery in transcriptomic or metatranscriptomic data, RdRpCATCH scans nucleotide or amino acid sequences specifically for RNA-dependent RNA polymerases using profile HMMs. After candidate viral sequences are identified, CheckV assesses the quality, completeness, and contamination of single-contig viral genomes, trimming integrated microbial flanking regions and validating terminal repeats; however, CheckV is an evaluation tool rather than a de novo identifier and expects candidate viral contigs as input.
For bacteriophage assemblies requiring functional annotation, Pharokka predicts coding sequences, tRNAs, and CRISPR arrays, using phage-specific gene prediction via PHANOTATE and functional profiling with PHROGs, CARD, and VFDB. Pharokka also supports alternative genetic codes via Pyrodigal-gv and RNA phages with Pyrodigal-rv. In contrast, while geNomad provides broad functional markers such as conjugation genes and antimicrobial resistance, its marker database focuses on classification utility rather than exhaustive functional annotation.
Downstream biological characterisation depends heavily on assembly completeness and target taxonomy. BACPHLIP determines whether a phage is temperate or virulent using conserved protein domains, yielding continuous probabilities, but requires complete genomes and is primarily trained on Caudovirales infecting Actinobacteria, Gammaproteobacteria, and Bacilli. For taxonomic classification, taxmyPHAGE assigns complete dsDNA bacteriophage genomes to genus and species according to official ICTV criteria, whereas geNomad assigns broader viral taxonomy but cannot classify sequences past the family level. Furthermore, taxmyPHAGE is not suitable for fragmented contigs, metagenomic assemblies, eukaryotic viruses, or RNA/ssDNA phages.
Questions
Can I run these tools without a GPU or installing anything?
Yes. The research agent runs each of these on a machine of its own — some are preinstalled, others are set up the first time a task needs them — and reads the results back to you.
Can CheckV identify viral sequences directly from raw metagenomic assemblies?
No. CheckV is not designed as a de novo virus classifier and cannot identify viral contigs on its own. It requires upstream identification tools such as geNomad to identify candidate viral contigs before it can assess their completeness, contamination, and provirus boundaries.
Which tool should be used for species-level and genus-level taxonomy of bacteriophages?
taxmyPHAGE classifies complete dsDNA bacteriophage genomes to genus and species levels using official ICTV demarcation thresholds. geNomad provides viral taxonomy assignments, but its classifications do not extend past the family level down to genus or species.
Can BACPHLIP analyse fragmented or metagenome-assembled phage contigs?
No. BACPHLIP strictly requires complete phage genomes because incomplete or fragmented assemblies lack sufficient information for accurate lifestyle prediction. It also assumes the input sequence is a phage, meaning host or non-phage contigs will yield misleading classifications.
How does RdRpCATCH differ from geNomad when analysing metatranscriptomes?
geNomad searches broadly for viruses and plasmids across sequencing data by combining neural networks and marker-based scores. RdRpCATCH specifically searches for RNA viruses by identifying RNA-dependent RNA polymerase (RdRp) sequences using aggregated collections of profile HMMs, accepting both nucleotide and amino acid inputs.
How do CheckV and geNomad handle proviruses integrated into host bacterial chromosomes?
CheckV annotates contig genes as viral or microbial using hidden Markov models and computes an intergenic score across sliding gene windows to identify host-virus integration breakpoints, generating trimming coordinates. geNomad also predicts provirus integration within sequencing data and automatically excises integrated proviral sequences into designated output files.
Written from each tool's own documentation, as summarised on its page here. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.