BRC Analytics American Society for Virology 2026

ASV 2026

BRC-Analytics: A free, universally accessible environment for analysis of viral data

The future is agentic

Anton Nekrutenko | Penn State | galaxyproject.org

gxy.io/asv26

BRCs = BV-BRC (bv-brc.org) + PDN (pathogendatanetwork.org) + BRC-analytics (brc-analytics.org)

BRC Analytics American Society for Virology 2026

Outline

A 15 min impossible challenge

  • What is BRC-Analytics
  • What is Galaxy
  • What are agentic analyses
  • Teaser: Logan / Search Entire SRA
BRC Analytics American Society for Virology 2026

BRC-Analytics: data, tools, workflows, infrastructure

brc-analytics.org

Data

NCBI Datasets · NCBI Virus · EBI · UCSC Genome Browser

Tools + Workflows

BioConda · BioContainers · Workflows

Compute and Storage

TACC · IU JetStream2 · ACCESS-CI

Agents
BRC Analytics American Society for Virology 2026

BRC-Analytics flow

brc-analytics.org

1
Find organism

Pick from 1,920 taxa.

Selecting a species in BRC Analytics

2
Select genome

Choose among 5,060 assemblies.

Selecting a genome assembly

3
Select workflow

Best-practice, community-maintained.

Selecting an analysis workflow

4
Select data

Anything in the SRA, or your own.

Selecting input data

5
Run workflow

One sample or a million.

Running the workflow in Galaxy

6
Interpret

Inspect, iterate, publish.

Interpreting results

BRC Analytics American Society for Virology 2026

Examples of workflows

available at brc-analytics.org

BRC Analytics American Society for Virology 2026

An example workflow

Also see iwc.galaxyproject.org

BRC Analytics American Society for Virology 2026

Galaxy is a free public resource and it scales

https://galaxyproject.org

750,000jobs per month
400,000+registered users
1,500concurrent users
$2,000,000+free compute / year
10,000+analysis tools
22,000+citations
BRC Analytics American Society for Virology 2026

Get data, run tools, run workflows, interpret

1 · Get your data — computer, web, SRA, anywhere

2 · Run a tool — select from 1,000s of tools

3 · Or run a workflow — 100s of curated workflows

4 · Interpret and publish — Jupyter, RStudio, soon agents

BRC Analytics American Society for Virology 2026

The future is Agentic!

AI is an environmental and social disaster … but it could be great for science if used responsibly

BRC Analytics American Society for Virology 2026

Responsibly? ... this is how we all go to hell

BRC Analytics American Society for Virology 2026

The bright agentic future

brc-analytics.org

Data

NCBI Datasets · NCBI Virus · EBI · UCSC Genome Browser

Tools + Workflows

BioConda · BioContainers · Workflows

Compute and Storage

TACC · IU JetStream2 · ACCESS-CI

Agents
BRC Analytics American Society for Virology 2026

Orbit

A BRC-Analytics / Galaxy agent

Orbit ~/chrM-variants
Chat▤ ⤓ ▥
1
Call chrM variants across these 4 samples on Galaxy.

Here's the plan — QC locally, then align and call variants on Galaxy. Approve to run.

chrM Variant Callinghybrid
  • ✓QC & adapter trimlocal
  • ✓Reference indexlocal
  • ✓Read alignmentgalaxy · bwa-mem2/2.2.1
  • ✓Variant callinggalaxy · bcftools_call
✓All 4 samples aligned (mean depth 812×). 27 variants pass filters — 3 are non-synonymous in MT-ND5.
NotebookActivityFile

Plan A: chrM Variant Calling hybrid

Question: how do mtDNA variants distribute across these tissues?

Steps
  • ✓1. QC & adapter trimfastp
  • ✓2. Reference indexbwa-index
  • ✓3. Read alignmentGalaxy · bwa-mem2/2.2.1
  • ✓4. Variant callingGalaxy · bcftools_call
loom-invocationcompleted
BWA-MEM alignment (chrM, 4 samples)
jobs 4/4usegalaxy.org
ready Galaxy CloudLocal Opus 4.8 notebook.md · git ✓
BRC Analytics American Society for Virology 2026

Example: Andes hantavirus glycoprotein

104 isolates, M segment. Does the rodent-to-human jump change what the virus may vary?

1
Pool hantavirus assemblies
2
Pool glycoprotein
3
Create codon-aware alignments of glycoprotein
4
Perform selection analysis with Datamonkey
71
217
598
649
899
1051
Gn Head
Gn Stalk
Gc Head
Gc Stem
TMD
1
512
648
1000
1137
BRC Analytics American Society for Virology 2026

We need testers!

You will be given API keys to frontier models!

forms.gle/T9EZyXBnACso6cYn6

BRC Analytics American Society for Virology 2026

One last thing: Logan

The entire public SRA, reassembled — available from Galaxy, and soon from BRC-Analytics directly

38Maccessions99.5% of SRA by size
87 Pbpraw reads inDec 2025 freeze
8.5 Pbpunitigs out
4 smedian queryone index · 186 Galaxy jobs
What it is

Every public SRA accession reassembled into unitigs — near-lossless, best for search — and contigs — error-corrected, best for alignment.

Read more here

What a virologist does with it
  • Query one viral sequence against ~23M libraries — at logan-search.org, or with kmindex_query in Galaxy.
  • Mine contigs for undescribed viruses — one search yielded 383 novel papillomavirus types across 105 hosts.
  • Screen public RNA-seq for latent virus; map host range from BioSample metadata.
Query it from Galaxy

kmindex_query on usegalaxy.org

Median 4 s against one index, 8.4 min against all of them.

Use it here

BRC Analytics American Society for Virology 2026

Thank you!

People A to Z

Artem Babayan, Dannon Baker, Kelsey Beavers, Danielle Callan, Rayan Chikhi, Nate Coraor, John Davis, Björn Grüning, Teo Lemane, Wolfgang Maier, Pierre Peterlongo, Sergei Pond, Dave Rogers, Marius Van Den Beek

Funding

NIH NIAID

NIH NHGRI

Links!

Find me at ASV26: anton@nekrut.org

gxy.io/asv26

BRCs = BV-BRC (bv-brc.org) + PDN (pathogendatanetwork.org) + BRC-analytics (brc-analytics.org)

Built from PLAN.md. 16 slides / 15 minutes.