Canada's IRIDA platform for genomic

epidemiology Gary Van Domselaar Chief, Bioinformatics

National Microbiology Lab

Public Health Agency of Canada

Integrated Rapid Infectious Disease Analysis informatics platform to support real-time infectious disease outbreak investigations

Open source, standards compliant, resource for public health agencies and researchers that complements other initiatives

Platform Overview

IRIDA

Servlet Co

ntain

er

REST API Central File

Storage

Web Interface

Ap

plicatio

n Lo

gic

Compute Cluster

Galaxy

$ ~ >_ Galaxy

Getting data into IRIDA

• Manual web interface upload

• Automated instrument upload (Illumina MiSeq)

Data Management

User Access Control System User Management

Project User Management

Getting data out of IRIDA

• Sharing project data

• Downloading

• Export to external Galaxy instance

• Exporting to the command-line

NCBI SRA Upload

NCBI SRA Upload

Accession

Data Sharing

Project X

Project Y

Project Z

Data Analysis

Galaxy

Assembly Tools

Variant Calling Tools

…

API

Worker Worker

IRIDA

…

Kmer=99 Min=500

Assembly

Sample Selection

Galaxy

Assembly Tools

Variant Calling Tools

…

API

Worker Worker

IRIDA

…

Kmer=99 Min=500

Assembly

Pipeline Selection

Galaxy

Assembly Tools

Variant Calling Tools

…

API

Worker Worker

IRIDA

…

Kmer=99 Min=500

Assembly

Analysis Execution

Galaxy

Assembly Tools

Variant Calling Tools

…

API

Worker Worker

IRIDA

…

Kmer=99 Min=500

Assembly

Variant Consolidation

HGT & Recombination

Filtering

Repeat region filtering

Meta-alignment generation

SNV Matrix

Whole Genome Phylogeny

Isolate Sequencing

Reads Variant Calling

Isolate Sequencing

Reads Variant Calling

The IRIDA SNVPhyl Pipeline

User

selects isolates

Phylogeny Viewer

…

selects reference

Reference Genome

Analysis Results

Automated Assemblies

Analysis Provenance

Auditing • Every creation,

modification, or deletion of data is audited.

• Data can be restored on accidental deletion or modification.

• Trace back data to justify decisions.

Sequencing Quality Control

Analytical Tool

Quality Control Module

Quality Metrics

Quality Control

Analysis QA/QC Model

Types of (Meta)Data Standardized Within IRIDA

Lab Analytics Genomics, PFGE

Serotyping, Phage typing MLST, AMR

Sample Metadata Isolation Source (Food, Host

Body Product, Environmental), BioSample

Epidemiology Investigation Exposures

Clinical Data Patient demographics, Medical

History, Comorbidities, Symptoms, Health Status

Reporting Case/Investigation Status

“Not just what data IS collected, but what SHOULD be collected”

Tools: GenGIS

Coming Soon: CARD – Comprehensive Antibiotic Resistance Database

Coming Soon: The Salmonella In Silico Typing Resource (SISTR)

SISTR: THE SALMONELLA IN SILICO TYPING RESOURCE │

https://lfz.corefacility.ca/sistr-app/ 25

In silico analysis of WGS data assembly statistics serovar prediction in silico typing (MLST, cgMLST) AMR prediction

Comparative genomic analyses cgMLST accessory gene content core SNPs

Epidemiologic analysis geospatial distribution temporal distribution source association

Coming Soon: IslandViewer and IslandCompare

Outbreak investigation Routine surveillance

PulseNet Canada Deployment

http://irida.ca

Contact

• Project Information: http://www.irida.ca

• Project source:

– https://github.com/phac-nml/irida

– https://github.com/phac-nml/irida-miseq-uploader

– https://github.com/phac-nml/irida-galaxy-importer

• Documentation: https://irida.corefacility.ca/documentation/

• E-mail: IRIDA-mail@sfu.ca

• IRC: #irida on irc.freenode.net

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