Users Exploring Results

Exploring results

Status: IN PLACE — these views are the daily working surface of the application. (Screenshots are COMING to this page; the origin README referenced UI captures that were never committed to the repository. The descriptions below are complete without them.)

A run's page is the working surface: run-level configuration, per-stage launch controls (full pipeline or any single stage, DADA2 substages included), and per-stage status. Long jobs report progress over a live server-sent event stream; the jobs panel watches or cancels them.

QC

Raw-read QC (FastQC aggregated by MultiQC) and the DADA2 quality, denoising, merging and taxonomy diagnostics are embedded in the UI, each with its relevant configuration alongside and a re-run control. This is the first place to look when retention numbers surprise you.

Results explorer

The run's merged taxonomy-and-count table, and derived tables, browsed interactively:

• per-column filters — text search, numeric range, include/exclude lists — and a global text filter;
• sorting, configurable pagination, column visibility with taxonomy-source presets (VSEARCH-only, DADA2-only, all) and a switch for the per-sample count columns;
• sequences carry BLAST links; OTU rows expand to their constituent sequences;
• filters save as named presets (config/presets/) and reapply; tables export to Excel (.xlsx) or save back into the run.

Lab professionals: column presets + saved filters give you standard views per assay — build the view once, share the preset. The OTU drill-down is how you audit what a cluster contains before reporting it.

Annotation

The annotation view applies a functional database (funcdb) to the merged table, independently per classifier (VSEARCH and DADA2). For each sequence: functional metadata (function, associated organism and material, environment, pathogen status, notes) down to a configurable maximum rank; a consensus rank (finest rank where the classifiers agree); and a composite confidence score (DADA2 bootstrap at that rank × vsearch percent identity) — which is deliberately labelled curiosity-grade, not a calibrated probability.

Curation, in place:

• Contamination tagging — yes / no / unassigned per taxon at a rank, with a live summary of affected reads.
• Manual BLAST assignment — override one sequence inline.
• FuncDB ledger — new functional entries, prefilled from the selected row, append to a ledger available to later annotation runs. Your edits survive re-annotation.

Lab professionals: contamination tagging is your decontamination audit trail — flags apply to every row sharing the rank and taxon, and the affected-read summary is the number to put in the QC record.

Composition

Per-sample or pooled stacked bars of ASV/OTU counts by biological category (protozoa, helminths, fungi, host, plants, invertebrates — the default set in config/composition.yml; sets and their named filters are editable from the Compositions page under SYSTEM). A category summary precedes the chart; a quality filter caps unresolved taxonomic placeholders.

Cross-run comparison

Across runs within a study: alpha-diversity comparison boxplots with significance testing, taxon overlap as proportional Euler or UpSet plots, NMDS ordination and PERMANOVA, and pipeline-stage read summaries — see Analysis and Statistics Today for what the statistics behind those charts claim.

Coming to this area

• COMING: CladeCumulus (#6) — a cumulative cladistic explorer with epistemic colour coding (scaffolded in src/analysis/clade_cumulus.jl); Full Evidence Mode (#7) — epistemic editor and fibre visualiser.
• COMING: Euler/UpSet visualisations and chart-editor parity in the Stipple UI migration (docs/migration/STATUS.md names these as the major parity risks).