Viruses and CRISPR · What you can do here
Check viral genome completeness and contamination
Assess viral genome completeness, host contamination and MIUViG quality tiers with CheckV. Establish whether your sequences represent complete genomes or fragments before downstream annotation.
What this involves
In viral genomics, establishing sequence quality is required before annotating genes or inferring taxonomy and lifestyle. Answering these questions out of order leads to confident errors. Assessing quality with CheckV determines sequence completeness, flags host contamination, and assigns each contig to a Minimum Information about an Uncultivated Virus Genome (MIUViG) quality tier.
When working from metagenomic assemblies, viral contigs and proviruses integrated into host bacterial DNA should first be resolved with geNomad. CheckV takes these candidates, trims flanking host sequence from proviruses, and compares the viral segments against its curated reference database to measure completeness and check for non-viral contamination.
The platform executes these tools directly on a dedicated machine where reference databases persist under /work. The agent chains inputs and outputs between geNomad and CheckV, returning trimmed viral sequences and quality metrics without requiring local software or database management.
How it goes
- 1Identify candidate viral contigsFor uncharacterised assemblies, run geNomad to identify viral sequences, assign marker-based scores, and locate integrated provirus coordinates.
- 2Prepare reference dataRun the setup job for CheckV on the host machine to make its 1.7 GB reference database available in the persistent workspace.
- 3Assess completeness and contaminationRun CheckV against your FASTA sequences, accession, or geNomad output to estimate genome completeness and flag host contamination.
- 4Evaluate MIUViG quality tiersInspect the completeness method and quality tier assignments, and pass the trimmed provirus outputs forward for downstream annotation.
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
- Completeness is relative to a reference database, so a genuinely novel phage with no close relative will score low for lack of a comparator rather than missing sequence.
- Always inspect the completeness_method field before citing a completeness percentage, and report the MIUViG quality tier as the summary.
- Do not pass untrimmed contigs to downstream annotation tools; always use the host-trimmed provirus sequences generated by CheckV.
- Never run lifestyle prediction tools like BACPHLIP on incomplete fragments, as they infer virulent lifestyles from the absence of lysogeny domains and will produce falsely confident results.
What it runs
Programs
- 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.
Questions
Do I need to install anything to check viral genome completeness and contamination?
No. The research agent does this work on a Linux machine of its own — it runs CheckV, geNomad there, keeps the files, and reads the results back to you. Long runs continue if you close the page.
Why does my phage show low completeness despite assembly evidence of a full circular contig?
CheckV estimates completeness by comparison with reference genomes. If your phage represents a genuinely novel lineage with no close relative in the database, it receives a low completeness estimate because comparators are missing, not because sequence is absent.
What sequence formats and inputs does CheckV accept on the platform?
You can supply an NCBI nucleotide accession such as NC_001416.1, a FASTA file uploaded to /work/uploads/, or an HTTP URL to a plain or gzipped sequence file. NCBI assembly accessions (GCF_) must have their genomic FASTA retrieved first.
Why must CheckV be run before functional annotation or lifestyle prediction?
Downstream tools rely on genome completeness. For instance, Pharokka should annotate host-trimmed proviruses rather than raw bacterial contigs, and BACPHLIP assumes unobserved lysogeny markers mean a phage is virulent, which is only valid on complete genomes.
How are integrated proviruses handled during quality estimation?
When geNomad identifies proviruses within host scaffolds, CheckV uses those coordinates to excise host contamination and trim the viral region before evaluating completeness.
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.