introduction to galaxy (ueb-uat bioinformatics course - session 2.2 - vhir, barcelona)

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Vall d’Hebron Institut de Recerca (VHIR)

Alex Sánchez

15/05/2014

Institut d’Investigació Sanitària acreditat per l’Instituto de Salud Carlos III (ISCIII)

Introduction to Galaxy

A web-based genome analysis platform

BIOINFORMATICS FOR

BIOMEDICAL RESEARCH

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• Galaxy overview and Interface

• Getting Data in Galaxy

• Analyzing Data in Galaxy

– Quality Control

– Mapping Data

• History and workflow

• Galaxy Exercises

NGS Analysis Using Galaxy

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What is Galaxy

• Galaxy is an open-source framework for integrating various computational tools and databases into a cohesive workspace.

But it can also be seen as

• A web-based service, integrating many popular tools and resources for comparative genomics.

And also

• A completely self-contained application for building your own Galaxy style sites.

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http://galaxyproject.org

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Galaxy Conceptual Framework

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Galaxy Interface Sections

contains links to

the downloading,

preparation and

analysis tools.

The center column

is where the

menus and data

will appear

show you the history of your analysis steps,

allow you view data and results, and more.

Register User

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Getting Data

Click Get Data

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Getting Data: Table Browser

Get Table Main

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Getting Data: UCSC Table Browser

Get Output

clade: Mammal genome: Human

assmbly: [current]

group: Genes and… track: UCSC Genes

table: knownGene

region: position, chrX

Output format: BED, and check Send output to

Galaxy

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Getting Data: Upload File

Upload File

Execute

File Format

Species

Upload or paste file

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Getting Data: Upload File

Specify multiple URLs

into the "URL / Text" box

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• Sequences and Alignment Format • Galaxy overview and Interface • Getting Data in Galaxy • Analyzing Data in Galaxy

– Text Manipulation tools – Filter and Sort – Operate on Genomic Intervals – Quality Control – Mapping Data

• History and workflow • Galaxy Exercises

NGS Analysis Using Galaxy

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Text Manipulation Tools

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Filter and Sort

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Operate on Genomic Intervals

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Fasta Manipulation

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Analyzing Data: Next Generation Sequencing

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Analyzing Data: Next Generation Sequencing

FASTQ file manipulation,

like format conversation,

summary statistics,

trimming reads,

filtering reads

by quality score…

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Analyzing Data: Next Generation Sequencing

Input: sanger FASTQ

Output: SAM format

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Analyzing Data: Next Generation Sequencing

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• Sequences and Alignment Format

• Galaxy overview and Interface

• Getting Data in Galaxy

• Analyzing Data in Galaxy – Quality Control

– Mapping Data

• History and workflow

• Galaxy Exercises

NGS Analysis Using Galaxy

22 Copyright OpenHelix. No use or

reproduction without express written

consent

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History: History Options

List saved histories and shared histories.

Work on Current History, create new, clone, share,

create workflow, set permissions, show deleted datasets or delete history.

List saved histories

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Workflow

Creates a workflow, allows

user to repeat analysis using different datasets.

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• Sequences and Alignment Format

• Galaxy overview and Interface

• Getting Data in Galaxy

• Analyzing Data in Galaxy – Quality Control

– Mapping Data

• History and workflow

• Galaxy Exercises

NGS Analysis Using Galaxy