What the Phage | Genomic Explorer

Select a Sample

No Data Loaded

The report container is ready. Please inject JSON payloads using the processing pipeline.

Total Contigs

Shortest Sequence

Longest Sequence

Note: Detailed results can be explored via the Tabs in the upper right corner

Summary across sample

Contig	Length	Quality (Completeness)	Identification overview	Taxonomy	Host	Annotation

Identification Overview Legend:

Score ≥ 0.85

0.5 < Score < 0.85

Score ≤ 0.5

Nothing found

Contig Quality Summary

CheckV results and viral sequence metrics

Phage Identification Overview

How to interpret the data

WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output; instead, they generate categories with likelihoods or directly predict and assign the contigs as phage.

The tool’s output and what WtP assigns are shown in the table below.

Explanation tool output

Output of each tool and the values WtP assigns in the table above.

Tool	Standard output	WtP displayed value	F1 scores by Ho et al.
deepvirfinder	score: 0 to 1	0 to 1	>0.83
metaphinder	string: phage	1	>0.83
metaphinder own	string: phage	1	N/A
phigaro	score: 0 to 1	0 to 1	N/A
pprmeta	phage_score: 0 to 1	0 to 1	0.92
seeker	score: 0 to 1	0 to 1	<0.5
sourmash	similarity: 0 to 1	0 to 1	N/A
vibrant	prediction: virus	1	>0.83
vibrant-virome	prediction: virus	1	N/A
virfinder	score: 0 to 1	0 to 1	>0.83
virnet	score: 0 to 1	0 to 1	N/A
virsorter	category 1, category 2, category 3	1, 0.5, 0	>0.83
virsorter-virome	category 1, category 2, category 3	1, 0.5, 0	N/A
virsorter2	dsDNAphage: 0 to 1	0 to 1	0.93

Tool Score Heatmap

Phage identification scores per contig and tool (0–1)

Upset Plot - Tool Intersection

Visualization of shared contig identifications across tools

How to Read This Plot

Interaction Matrix: The grid of dots at the bottom shows combinations of tools. Connected black dots form an "intersection" (a specific set of tools that agreed).
Vertical Bars: The height of each bar represents the number of contigs identified exclusively by that specific combination of tools.
Horizontal Bars: Show the total number of contigs identified by each tool individually (Set Size), regardless of overlap with other tools.

Combined Taxonomy Findings

Comparison of Sourmash, GeNomad and Taxmyphage results

Contig	Sourmash Sim.	Sourmash Tax	Genomad Agree.	Genomad Lineage	Taxmyphage Genus

Tool algorithms

Sourmash: k-mer based similarity to a reference genome

Genomad: marker-gene based agreement and lineage

Taxmyphage: predicted genus from ICTV-based genome clustering

Sourmash Details

K-mer based taxonomic classification

Contig	Similarity	Accession	Taxonomy	Host	Lifestyle

GeNomad Details

Marker gene based taxonomy

Contig	Agreement	N Genes	TaxID	Lineage

Taxmyphage Details

Genome similarity based taxonomy

Genome	Realm	Kingdom	Phylum	Class	Order	Family	Subfamily	Genus	Species	Full Taxonomy	Message

Genome Viewer

Visualizing annotations on Sequences

Compare

Show Labels

Genome Viewer Features

Compare Mode: Select multiple contigs to visualize them stacked together in the Linear Viewer.
Circular View: Provides a circular plasmid map of a specific contig generated by a single specific tool.
Interactive Legend: Click on any functional category in the legend below to show/hide the gene labels for that category.
Details on hover: Hovering over any gene segment on the map will display a popup with exact locations and details.

Select a contig to view annotations

Annotation Details

Full list of annotated features

Contig	Start	End	Strand	Feature	Tool

Prophage Overview

Consolidated prophage predictions per contig across tools

How to interpret this table:

PhaBOX2 Cand = number of candidate provirus regions

PhaBOX2 Contam = provirus status (Yes / No) + purity classification

VirSorter2 = best viral score group + confidence

Phigaro / Genomad Regions = prophage regions detected

Total Regions = sum of PhaBOX2 Cand + Phigaro + Genomad

PhaBOX2 Candidate Provirus

PhaBOX2 Contamination Prediction

VirSorter2 Final Viral Score

Phigaro Prophage

GeNomad Filtered Provirus

Phage lifecycle prediction

BACPHLIP and PhaBOX PhaTYP-based lifecycle prediction

How to interpret this table:

BACPHLIP

bacphlip_Virulent & bacphlip_Temperate = classifier probabilities (0–1)

bacphlip_prediction = predicted class (virulent / temperate)

PhaBOX PhaTYP

phatyp_TYPE = predicted lifecycle (virulent / temperate / ambiguous)

phatyp_PhaTYPScore = confidence score (0–1)

Consensus

virulent

temperate

disagree

BACPHLIP Lifecycle

Random forest classifier probabilities

PhaBOX PhaTYP Lifecycle

Deep learning based lifecycle prediction

Combined Host Predictions

Phabox2 and iPHoP predictions per contig

Phabox2 Host Prediction

Predicted host organisms based on genomic similarity

How to interpret this table:

Phabox2 Score

Score ≥ 0.8 (high confidence)

0.6 ≤ Score < 0.8 (moderate confidence)

Score < 0.6 (low confidence)

Lineage

Host NCBI / GTDB lineage shown from domain to species

iPHoP Host Prediction

Host prediction to genome (m90) database

How to interpret this table:

Confidence ≥ 80% (high)

60% ≤ Confidence < 80% (moderate)

Confidence < 60% (low)