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Total Contigs
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Shortest
Sequence
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Longest
Sequence
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Note: Detailed results can be explored via the Tabs in
the upper right corner
Summary across sample
Contig
Length
Quality (Completeness)
Identification overview
Taxonomy
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
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.
Sourmash Hits
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Genomad
Hits
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Combined Taxonomy Findings
Comparison of Sourmash and GeNomad results
Contig
Sourmash
Sim.
Sourmash Tax
Genomad
Agree.
Genomad Lineage
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
Genome Viewer
Visualizing annotations on Sequences
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.