A modern open-source platform that transforms bioinformatics workflow outputs into interactive dashboards.
Build, share, and explore data visualizations with or without writing code.

Bioinformatics pipelines produce more output than anyone reads. Depictio turns that output into dashboards you can hand to a collaborator, from any execution engine: Nextflow, Snakemake, Galaxy or a shell script.

Workflow Ecosystem

Connect with standardized bioinformatics workflows from various platforms.

Snakemake Workflow Catalog

Depictio in numbers

42

nf-core pipeline templates

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All templates →

135tools · 465 outputs

in the Tools Catalog

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• salmon
• deseq2
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• star
• samtools
• pangolin
• bcftools
• nextclade

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• salmon
• deseq2
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• star
• samtools
• pangolin
• bcftools
• nextclade

• kallisto
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• busco
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• metaphlan
• edger
• macs2
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• cellranger

• kallisto
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• busco
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• metaphlan
• edger
• macs2
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• cellranger

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• snpeff
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• dexseq
• mosdepth
• cellbender
• picard
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• snpeff
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• dexseq
• mosdepth
• cellbender
• picard
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• deeptools
• simpleaf
• arriba
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• cnvkit
• cooltools
• nanoplot
• damageprofiler
• bismark

• deeptools
• simpleaf
• arriba
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• cnvkit
• cooltools
• nanoplot
• damageprofiler
• bismark

Open the catalog →

2,176

ready-made renders

• Card 942
• Advanced viz 414
• Table 391
• Figure 245
• Interactive 123
• MultiQC 61

See the renders →

56

advanced visualizations

Each with its own controls and views

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See them all →

As of v1.20.0

Dashboard Components

Pick a component to see a few examples from real dashboards. Most are live: hover, zoom and use their controls.

FigurePlotly charts, any kind Advanced vizOmics plots with controls CardMetrics at a glance TableSort, filter, export InteractiveFilters for every tile MultiQCYour QC report, live MapSamples on a map Genome browserTracks next to the dashboard TextNotes for the reader ImageGalleries from S3

Figure

DistributionScatter + marginalsViolinBoxDots + thresholds Lines & pointsAnnotated linesProfileShaded bandsMA scatterGenome scatter MatrixHeatmapAnnotated grid CompositionStacked barsGrouped barsScore breakdown LayoutShared axisFacetsGenome-wide

• Scatter, bar, line, histogram, box and ComplexHeatmap from the editor
• Code mode takes any Plotly Express call
• A click or a lasso on a scatter filters the dashboard

Figure docs →

Advanced viz

MatrixAnnotated heatmapUpSetOncoplotSignal matrix GenomeCoverage + annotationCopy numberChordIdeogramSashimi ProteinLollipopFusion structureHMM logoAlignment3D structure StatisticsVolcanoManhattanRankedDot plot Hierarchy & flowSunburstSankeyStacked taxonomyRarefaction

• 56 visualizations: volcano, oncoplot, sunburst, genome tracks, 3D structures and more
• Each comes with its own controls; some switch between views

Advanced viz docs →

Card

Overview styles

• One metric per card: count, sum, average, median, unique values and more
• A secondary view shows its shape: donut, box plot, sparkline, histogram, gauge
• Follows every filter on the dashboard

Card docs →

Table

Abundance

• AG Grid with server-side paging, so large tables stay fast
• Sort and filter by column, export to CSV
• Selecting rows filters the dashboard

Table docs →

Interactive

Linked filters Filters in action Filter panel

• Range slider, slider, multi-select, date picker, segmented control, text search
• Each filter applies to every linked component
• Grouped in a filter panel at the side of the dashboard

Interactive docs →

MultiQC

PlotsStatus heatmapCoverage linesInsert sizeStacked barsVariant effects TableGeneral stats

• MultiQC plots and the general stats table, inside the dashboard
• Filtered with the rest of the dashboard

MultiQC docs →

Map

Sampling sites

• Tile maps from latitude and longitude columns, no API key
• A click or a lasso on the sites filters the dashboard

Map docs →

Genome browser

Tracks Navigator

• JBrowse 2 inside the dashboard, no browser server to run, bound to a manifest of track files: bigWig, BAM, VCF, BED, GFF
• GenomeSpy lanes (the Navigator) show every library along the genome, here coloured by time point: brush a region and the browser opens on it
• The browser's window is drawn as a band on the lanes, and a click on a feature filters the dashboard on its sample
• Filters pick the tracks and frame the locus

Genome browser docs →

Text

Overview Study & run

• Markdown blocks between the plots
• Say what the dashboard answers and how to read it
• Values computed from the data and the run parameters, kept up to date

Text docs →

Image

Cell Painting

• Image galleries served from S3 or MinIO storage
• Filtered by the dashboard's interactive components
• Click a thumbnail for the full-size image

Image docs →

A selection, not the full list: each component has more types, options and layouts. See all components and the advanced visualizations.

Live interactive demo - Try it!

The dashboard below is the output of an nf-core/ampliseq run, ingested with the CLI and built from a pipeline template. The demo signs you straight into a temporary account, so you can browse the pre-loaded projects and create your own without registering.

Note: Accounts and related data will be reset after 1 hour to keep the demo environment clean.

Get started with Depictio

Try Demo Directly Open in Codespaces Install Locally

Live Demo

Key Features

From the command line that reads your pipeline output to the instance an admin runs in production.

01Your data, in one placeProjects →

Project & template

One pipeline, many runs, one place

A project holds the workflows, the data collections and the dashboards that belong together. Declare it in a YAML file or build it from the browser, whichever suits the run. A template turns that declaration into a reusable recipe: one command against a new run of the same pipeline and the whole thing stands up again, project, data collections and dashboards included, ready to read.

What a project is → Templates →

Upload

Or just drop the file in

No pipeline to point at yet? Drop a CSV, TSV, Parquet or Feather file straight into a project from the browser, or a MultiQC report, and Depictio scans it and aggregates it into a Delta table for you. The collection is ready to build on without touching the CLI, and you can link two of them on a shared column from the same screen, so a filter on one reaches every component built on the other.

Start a project →

Ingest

Read where your data lives

Point depictio ingest at a finished run, on your laptop or on the cluster where it landed, and it scans the output in place, pushing only the aggregated results, never the raw files. Smaller collections can be added straight from the browser instead. Either way the ingestion report says what was found, what was missing, and the parameters the pipeline ran with.

Ingest with the CLI →

Nextflow trigger

Or let the pipeline ingest itself

Install the trigger once on the machine that runs nextflow, and a pipeline that completes is ingested into Depictio on its own, with the template picked from the pipeline's name and version and not a line about Depictio in the pipeline. Install it opt-in with --default-disabled and only the runs that pass --depictio_enabled true are ingested. A failed run is never ingested, and a problem on Depictio's side leaves the pipeline's exit status alone.

Nextflow trigger →

02Build the dashboardBuild a dashboard →

Build

Drag, drop, resize

Every component sits on the same grid: drag one anywhere, pull its corner to resize it, and the cards around it move out of the way. Figures, tables, metric cards, image galleries, maps, text, filters and MultiQC panels all behave the same way, and the layout is saved as you go. Nothing here needs code.

Add a component →

Design

Design your component

Adding a component starts with a choice, and this is the first branch: pick the type, connect it to a data collection, then tune it against a live preview. Axes, colours, layout, cross-filtering, and Code Mode when you want the Plotly figure itself.

Build a dashboard →

Catalog

Or take one off the shelf

The other branch: the tools catalog recognises which tool produced each output in your project and offers the visualizations that tool is known to support, pre-configured and previewed at the exact grid box the component will occupy.

Pick from the catalog →

$ depictio dashboard export \ <id> -o dashboard.yaml

dashboard.yaml

components:
  - component_type: card
    data_collection_tag: metadata
    column_name: sample_id
    aggregation: nunique
  - component_type: advanced_viz
    data_collection_tag: ancombc
    viz_kind: volcano

$ depictio dashboard import \ dashboard.yaml

YAML

Or write the dashboard as code

Export any dashboard to a YAML file, review it in a pull request, and import it back into another instance. Sections, filters and every component are plain fields, so a change to a dashboard reviews like any other change.

Dashboards as YAML →

Organise

Room for a real dashboard

Group cards into sections, keep one filter panel across a family of tabs, dock a map beside the data, and inspect any component to see where its numbers come from.

Sections and tabs →

Versions

Go back to any version, data included

Every change to a dashboard is kept as a version: bookmark one, share it as a read-only preview link, restore it, or bring back a single component. A version also records which commit of each table it drew from, so a past dashboard is shown with the data it showed at the time, and the editor can draw today's layout from earlier data.

Dashboard and data versions →

03Read the scienceComponents →

Visualize

Plots built for omics

Volcano, Manhattan, UpSet, hierarchical heatmaps, phylogeny, ordination and many more, alongside the usual scatter and bar charts. Each one is an advanced viz: you bind it to any table or file whose columns fit it, rather than waiting for the tool that produced the data to draw it for you.

Every advanced viz →

Explore

Pick a clade, filter everything

Click any internal node and the panel names what you picked: how many tips it holds, how deep it runs, how well the branch is supported, and how those tips break down by taxonomy. Send it through as a filter and every other component on the dashboard narrows to the same samples.

Phylogeny interaction →

MultiQC

Every QC report, in the dashboard

Hand Depictio the MultiQC reports a run produced, from the CLI or straight from the browser, and it aggregates them across every sample and every run; and their data becomes components you place like any other: General Statistics as a table, each module's plot as its own card. Then it goes past what the HTML report can do: join those panels to your sample sheet and to any other collection in the project, and filter all of them at once from your own metadata, from a map, from a date picker, or from any other filter component on the dashboard.

Working with MultiQC →

Group

Slice it, then compare

Lasso points on a plot, pick rows in a table, or select a region on the map, then save what you picked as a named group. Every component on the dashboard then colours by that grouping at once, or splits into one panel per group, so treated and control sit side by side instead of in two browser tabs. Groups survive a reload and travel with the dashboard, so the comparison is something you share rather than something you rebuild.

Selection groups →

Map

Where the samples came from

Any collection carrying coordinates becomes a map: points, choropleths from your own GeoJSON, or a panel that follows you across every tab. Dock it in the filter rail or float it over the grid, and lasso a region to filter every other component down to the samples inside it, exactly like a dropdown would. Geography stops being a column in a table and becomes a way to ask questions of the run.

The map panel →

04Run it, extend itAdministration →

Live

Watch a run as it lands

Opt a project into real-time events and its dashboards hold a WebSocket open. Each time the CLI ingests new data the server broadcasts on that channel and the affected components refresh themselves, with no reload and no polling. A log beside the grid lists the events as they arrive, so you can watch a run fill a dashboard in while it is still running.

Real-time events →

Operate

Run your own instance

Depictio is meant to be self-hosted, and the admin panel is built for that: scheduled backups with a retention policy and a restore gated behind validation, tasks, ingestion runs, logs and service health in one view, users and groups, and branding that reaches the whole instance, its name, its logo, its palette, the login screen and the figures it renders.

Monitoring and tasks →

Tools catalog

Add your tool without writing YAML

And the shelf is yours to stock. Drop one output file, bind its columns in Depictio's own component builder, and Tool Studio writes the catalog entry and opens the pull request for you, so the next person picks what you designed.

Open Tool Studio →

Tools Catalog

Depictio recognises the bioinformatics tools behind your data and offers the visualizations those tools are known to support, ready to drop on a dashboard.

Browse the catalog

Every recognised tool, every output, and what each one renders as. Previewed on real fixture data.

Open the catalog →

Pick, don't build

Adding a component starts with a choice: build it yourself, or pick a pre-configured one the catalog matched to your data.

See the picker →

Contribute a tool

Tool Studio authors an entry in the browser: drop an output file, bind its columns, and it opens the pull request for you.

Open Tool Studio →

Getting Started

Ready to get started with Depictio?

Python package

Three commands, from results to dashboard

On a laptop and without Docker: install the package, start the server, then point it at a pipeline's output. The same server runs in Docker Compose or Kubernetes when a team needs it, and a local server moves to Docker Compose with its data.

Python package installation →

uv tool install "depictio[local]"
depictio local up
depictio ingest path/to/results

Live demo

Example dashboards, ready to explore

No sign-up

Codespaces

The Python package, in a cloud workspace

No install

Python package

Try it on a laptop, no containers

No Docker

Docker Compose

A shared instance for a team or a demo

Recommended

Kubernetes

For production environments

Production

CLI Tools

For data ingestion and management

Tools

Funding

Depictio is developed with the support of academic and public funding, enabling us to provide a free and open-source platform for the bioinformatics community.

Marie Skłodowska-Curie Grant

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 945405

Learn More

ARISE Programme

ARISE is a postdoctoral research programme for technology developers, hosted at EMBL.

Learn More

EMBL

The European Molecular Biology Laboratory is Europe's flagship laboratory for the life sciences.

Learn More

Academic Partners

SciLifeLab Data Centre

SciLifeLab Data Centre provides data-driven life science research infrastructure and expertise to accelerate open science in Sweden and beyond.

Learn More

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