# PathoGFAIR: collection of Galaxy FAIR workflows for pathogen detection and samples comparison

Engy Nasr, Anna Henger, Bjoern Gruening, Paul Zierep, Bérénice Batut

► To cite this version:

Engy Nasr, Anna Henger, Bjoern Gruening, Paul Zierep, Bérénice Batut. PathoGFAIR: collection of Galaxy FAIR workflows for pathogen detection and samples comparison. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. 10.7490/f1000research.1119769.1. hal-04644577v2

HAL Id: hal-04644577

https://hal.science/hal-04644577v2

Submitted on 11 Jul 2024

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Distributed under a Creative Commons Attribution 4.0 International License
PathoGFAIR

Collection of Galaxy FAIR Workflows
for Pathogen Detection & Samples Comparison

Presented by: **Engy Nasr** from the University of Freiburg

on behalf of all authors: Anna Henger, Björn Grüning, Paul Zirep and Bérénice Batut
# Food Contamination: A Global Health Threat

**Food pathogen:** A harmful microbe in food that can cause illness, including bacteria, viruses, parasites and fungi

Affects **600 million** people a year,
casing illness and even death

<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>
# Pathogen Detection Challenges

## Traditional Methods

PCR (Polymerase Chain Reaction)

Limited to a specific small DNA region

Needs of prior knowledge of DNA

<figure><img src="image_4.png" /></figure>

WGS (Whole Genome Sequencing)

Requires prior DNA isolation of a targeted pathogen

Time consuming

## Shotgun Metagenomics Approach: A Breakthrough

Analyzes all genetic material present in a complex sample, such as microbial communities in environmental or clinical samples.

Detects and identifies pathogens & studies interactions and functions between microbes.

<figure><img src="image_5.png" /></figure>

Copyright: Sanford doddlab
Nanopore sequencing enhances shotgun metagenomics for contamination investigations, offering real-time, long-read data for fast, accurate pathogen detection

Crucial for rapid responses
# Limitations of Other Pathogen Detection Approaches

Lack of available, accessible, free or easy-to-use pipelines, e.g. OneCodex, SURPI, and Sunbeam

So we introduce **PathoGFAIR**

a very cool and awesome series of **Galaxy-based 5 FAIR** workflows for
**Pathogen Detection**

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PathoGFAIR Workflows

<figure><img src="image_7.png" /></figure>

<footnote>* Easily adaptable to any other type of sequencing technique</footnote>
PathoGFAIR Workflows

<figure><img src="image_8.png" /></figure>

<footnote>* Easily adaptable to any other type of sequencing technique</footnote>
# PathoGFAIR Workflows

<figure><img src="image_9.png" /></figure>

<footnote>* Easily adaptable to any other type of sequencing technique</footnote>
# PathoGFAIR Workflows

<figure><img src="image_10.png" /></figure>

<footnote>* Easily adaptable to any other type of sequencing technique</footnote>
# PathoGFAIR Workflows

<figure><img src="image_11.png" /></figure>

<footnote>* Easily adaptable to any other type of sequencing technique</footnote>
PathoGFAIR is Awesome

Web Interface

PathoGFAIR workflows are deployable on all Galaxy servers, which have a wonderful user friendly web interface

Patho-
GFAIR

<figure><img src="image_12.png" /></figure>
PathoGFAIR is Awesome

PathoGFAIR is very easy to use, it requires **zero** computer science background, with a simple one mouse click, all analyses, results, visualisations and reports are out

<figure><img src="image_13.png" /></figure>

Patho-
GFAIR
# PathoGFAIR is Awesome

PathoGFAIR provides **reports** highlighting all findings from the performed analyses, which includes multiple interactive and non-interactive **visualisations**

Web Interface

User Friendly

Shareable
Reports &
Visualisations

Patho-
GFAIR

<figure><img src="image_14.png" /></figure>
PathoGFAIR is Awesome

PathoGFAIR is easily **adaptable** to any other
type of sequencing technique,
and **scalable** to thousands of datasets

Web Interface

User Friendly

Patho-
GFAIR

Shareable
Reports &
Visualisations

Easily
Adaptable &
Scalable
# PathoGFAIR is Awesome

PathoGFAIR has a training material on our
awesome Galaxy Training Network (GTN),

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

<figure><img src="image_17.png" /></figure>

Web Interface

User Friendly

Patho-
GFAIR

Shareable
Reports &
Visualisations

Training
Material &
Documentation

Easily
Adaptable &
Scalable
# PathoGFAIR is Awesome

PathoGFAIR has a training material on our awesome Galaxy Training Network (GTN), and a full documentation on PathoGFAIR GitHub repository

<figure><img src="image_18.png" /></figure>

PathoGFAIR-FAIR-Workflows-for-Pathogen-Detection-and-Samples-Comparison Public

<figure><img src="image_19.png" /></figure>

Pin

<figure><img src="image_20.png" /></figure>

Unwatch

<figure><img src="image_21.png" /></figure>

<figure><img src="image_22.png" /></figure>

Web Interface

User Friendly

Patho-
GFAIR

Shareable
Reports &
Visualisations

Easily
Adaptable &
Scalable

Training
Material &
Documentation
# PathoGFAIR is Awesome

PathoGFAIR has been tested successfully with 130 samples, with different pathogens, from different hosts and sequencing conditions

<figure><img src="image_23.png" /></figure>

Tested

Web Interface

User Friendly

Patho-
GFAIR

Shareable
Reports &
Visualisations

Easily
Adaptable &
Scalable

Training
Material &
Documentation
# PathoGFAIR is Awesome

All tools used in PathoGFAIR workflows have available free conda packages and are wrapped in Galaxy tool wrappers

BIOCONDA®

<figure><img src="image_24.png" /></figure>

<figure><img src="image_25.png" /></figure>

Web Interface

<figure><img src="image_26.png" /></figure>

User Friendly

<figure><img src="image_27.png" /></figure>

PathoGFAIR

<figure><img src="image_28.png" /></figure>

Shareable Reports & Visualisations

<figure><img src="image_29.png" /></figure>

Tested

<figure><img src="image_30.png" /></figure>

Training Material & Documentation

<figure><img src="image_31.png" /></figure>

Easily Adaptable & Scalable
# PathoGFAIR is Awesome

All 5 PathoGFAIR workflows are fully annotated, shared, and instantly deployable via the Intergalactic Workflow Commission (IWC), Dockstore and WorkflowHub

<figure><img src="image_32.png" /></figure>

WorkflowHub

<figure><img src="image_33.png" /></figure>
<figure><img src="image_34.png" /></figure>

<figure><img src="image_35.png" /></figure>

Packaged open source tools

BIOCONDA

<figure><img src="image_36.png" /></figure>

Explicit user friendly
workflow environment

<figure><img src="image_37.png" /></figure>

PROJECT

Freely available to be
directly run

<figure><img src="image_38.png" /></figure>

EUROPE

Annotated, shared and
deployable

<figure><img src="image_39.png" /></figure>

<figure><img src="image_40.png" /></figure>

WorkflowHub

Training and
Documentation

<figure><img src="image_41.png" /></figure>

<figure><img src="image_42.png" /></figure>

Tested successfully on
130 samples
# Thank You ...

## All authors

<figure><img src="image_43.png" /><figcaption>Engy Nasr</figcaption></figure>

<figure><img src="image_44.png" /><figcaption>Anna Henger</figcaption></figure>

<figure><img src="image_45.png" /><figcaption>Björn Grüning</figcaption></figure>

<figure><img src="image_46.png" /><figcaption>Paul Zierep</figcaption></figure>

<figure><img src="image_47.png" /><figcaption>Bérénice Batut</figcaption></figure>

## All Galaxy Freiburg Team specially

<figure><img src="image_48.png" /></figure>

<figure><img src="image_49.png" /><figcaption>Wolfgang Maier</figcaption></figure>

<figure><img src="image_50.png" /><figcaption>Mina Ansari</figcaption></figure>

## EOSC-Life For Funding

<figure><img src="image_51.png" /></figure>

EOSC-Life

## Special thanks to

<figure><img src="image_52.png" /><figcaption>Peter van
Heusden</figcaption></figure>

<figure><img src="image_53.png" /><figcaption>Tobias
Schindler</figcaption></figure>

<figure><img src="image_54.png" /><figcaption>Marius van
den Beek</figcaption></figure>

<figure><img src="image_55.png" /></figure>
Thank You

Questions?

Waiting for you all in the **Pathogen Detection Training**

Today at 13:00, Room: Congress hall B