Viruses and CRISPR · What you can do here
Annotate a phage genome online
Annotate bacteriophage contigs using Pharokka to identify protein-coding genes, PHROG functional categories, tRNAs, CRISPR arrays, and AMR or virulence markers.
What this involves
Bacteriophage annotation requires answering biological questions in a rigorous sequence. Before assigning gene functions, you must confirm that the sequence is viral and determine whether it represents a complete genome or an integrated provirus. Annotating raw metagenomic contigs without quality checks risks annotating host contamination or incomplete fragments.
The platform executes Pharokka on a dedicated machine using its local database (~1 GB). Pharokka calls genes and assigns them to PHROG functional categories, alongside scanning for non-coding RNAs, CRISPR features, and antimicrobial resistance or virulence determinants. It produces standard GenBank and GFF files that can be fed into downstream classification tools or structural re-annotation pipelines such as phold.
When working with proviruses integrated into bacterial hosts, annotation must be performed on trimmed proviral coordinates, such as those resolved by CheckV, rather than uncurated host contigs. The agent manages these tool dependencies and database downloads, writing outputs into a persistent workspace across turns.
How it goes
- 1Verify viral origin and completenessRun geNomad to confirm viral markers and CheckV to assess genome completeness, contamination, and proviral boundaries before beginning annotation.
- 2Prepare sequence inputPass an NCBI nucleotide accession, a local FASTA file, or a direct sequence URL; if using proviruses, supply the trimmed sequence resolved by CheckV.
- 3Execute Pharokka annotationPharokka identifies open reading frames, maps PHROG functional categories, and detects tRNAs, CRISPR arrays, virulence hits, and AMR genes.
- 4Export annotation outputsThe agent inspects the run and writes standard GenBank and GFF files into the workspace for inspection or downstream processing.
Start it here
Ask in plain language. The agent works on a Linux machine of its own — it installs and runs what the job needs, keeps every file, and reads the results back with the numbers explained. Nothing to set up, and a long run continues after you close the page.
What to watch for
- Most phage genes have no known function, and sixty to eighty percent hypothetical proteins is ordinary in a phage annotation.
- Do not present the annotated minority of genes as an exhaustively characterised genome.
- If annotating an integrated provirus, annotate CheckV's trimmed provirus coordinates rather than the raw bacterial contig.
- Prophage boundaries predicted by screening tools are approximate unless specific attachment sites have been identified.
- An assembly accession (such as GCF_) is not a direct nucleotide sequence and requires fetching the genomic FASTA before Pharokka can run.
What it runs
Programs
- PharokkaRuns as a job on its own machine· MITRapid, standardised genome annotation pipeline for bacteriophage isolates and metaviromes.
- CheckVRuns as a job on its own machine· BSD-3-Clause-LBNLA command-line pipeline for assessing the completeness, contamination, and quality of viral genomes from metagenomes.
- geNomadRuns as a job on its own machine· BSD-4-Clause (per the bioconda recipe; the repository's own LICENSE is not SPDX-tagged)Identifies plasmids and viruses in sequencing data, predicts proviruses, and assigns viral taxonomy.
- ProdigalPreinstalled on the research machineProtein-coding gene prediction software for bacterial, archaeal, and metagenomic DNA sequences.
nf-core pipelines
Questions
Do I need to install anything to annotate a phage genome?
No. The research agent does this work on a Linux machine of its own — it runs Pharokka, CheckV, geNomad, Prodigal there, keeps the files, and reads the results back to you. Long runs continue if you close the page.
What inputs does Pharokka accept on the platform?
You can provide an NCBI nucleotide accession (such as NC_001416.1), a path to a FASTA file in the workspace, or an accessible URL. Gzipped FASTA files are supported directly.
What functional annotations does Pharokka provide?
Pharokka provides gene calls annotated with PHROG functional categories, identified tRNAs, CRISPR arrays, and matches for antimicrobial resistance (AMR) and virulence genes.
Can I run PHASTEST or iPHoP here?
No. PHASTEST is an external web service with no runnable code, and iPHoP requires a reference database of several hundred gigabytes that is impractical to host on the environment.
How do I upgrade annotations with structural models?
You can follow Pharokka with phold, which accepts Pharokka's GenBank output and applies ProstT5 structural homology models running on CPU.
Written from the method the research agent follows for this work and the documentation of the tools listed above. Statements citing a figure that does not appear there are removed before publication. Corollary is a non-commercial research demonstration; results are not for clinical use.