Follow-up list
0
Star an organism to track it across every tab.
Detections
Organisms across the run (respects sidebar filters). Click a column header to sort · click a row to pin
for comparison.
● = high-consequence pathogen ·
Ⓓ/Ⓡ
= DNA / RNA ·
Strain
Species
Genus
= taxonomic level of each row ·
hover the spark for a coverage-depth
preview.
Click to target an organism for follow-up across tabs.
Genera Comparison Across Samples
Annotation Summary (VF / AMR)
Cross-Sample Organism Analysis
Aggregates every detection across the 0 sample(s) with a
positive hit (respects sidebar filters): how often each organism is seen, its TASS / coverage spread,
how samples cluster, and which organisms co-occur. Prevalence % is measured against all specimens with
any positive hit run-wide.
Sample × Organism — value heat
TASS Score by Organism (grouped by taxonomy)
Taxonomic Sunburst
Radial view of taxonomy sized by the selected metric. Click arc to zoom · center ring = up one level · ↺ =
reset to root
Coverage Scatter
Compare coverage, depth, reads, and TASS to spot outliers across samples.
Optional tab. This view appears when the run includes
--annotate, which
annotates the de novo assembly for virulence-factor, AMR, and transporter genes.
Virulence, AMR, and transporter gene hits summarized by genus, plus a searchable annotation table.
VF / AMR / Transporter Hits by Genus
Annotation Properties Distribution
Annotation Table
Category:
TASS:
✓Entry in run report
ExtExternal (not in run)
Optional tab. This view appears when a novelty backend is enabled, e.g.
--novelty kaiju (or --novelty mmseqs2 / --novelty bracken). The
active backend is shown in the badge to the right.
Reference-free / open-set novelty for the closed-set residual (reads that aligned to no reference,
assembled into contigs for contig-based classifiers). Each sample gets a novelty score (higher =
more divergent from known references) and a flag when that score crosses the run threshold. The
candidate table lists the genus-or-higher taxa the classifier could still assign. Use the
downloads for the raw per-sample / combined JSON and XLSX.
Novelty score — all samples
dashed line = flag threshold (~3). Hover points for details; drag a box to zoom x and y axes.
Per-sample novelty
Candidate taxa
Where the reads landed — alignment / TASS vs novelty rescue
Downloads
Contig / Assembly Read Distribution
Per-contig distributions for the selected organism and sample.
Explore
Cross-sample comparison plots for multi-metric patterns and relationships.
Multi-metric Radar
— normalized 0–1 per metric
Sample × Category Chord
— chord width = # reads aligned
Organism Rankings
— sorted by selected metric
Metric Correlogram
— pairwise Pearson correlation across the filtered rows
Full Detections Table
Complete list of detections across the run (respects sidebar filters). Click a column header to sort · click
a row to pin it · click the ★ to add to the follow-up watchlist.
● = high-consequence ·
Strain
Species
Genus
= taxonomic level of each row ·
↑ species
/
↑ genus
= below TASS cutoff, kept visible by parent roll-up ·
= meets TASS threshold independently ·
amber bar = rescued or pinned row
The metadata table. One row per sample — edit any cell, add columns, or upload a
metadata CSV. Adding
latitude / longitude (or
sample_origin_country / …state…) lights up the Mapping tab; a
collection_time column lights up Trends. The Group by bar
underneath is shared — whatever you pick here also drives the Mapping and Trends tabs.
Run Metadata
Click any cell to edit — saved with exported state.
Mapping. Plot samples at their coordinates or aggregate them by country / state.
Coordinates and geography come from the Metadata tab — the
metadata table is where you add or edit them.
Trends & group analysis. Time series, host / site breakdowns and the group-level
heatmap, network and cross-entry comparison. All of them read the Group by selection
below, which is shared with the Metadata and Mapping tabs.