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Using Galaxy for NGS Data Analysis

Olga Novikovaonovikova@albany.edu

Next-Generation Sequencing Bootcamp

Where to start?

You have FASTQ file. What is next?

Pay-to-play integrated solutions

From scratch

Free integrated solutions Galaxy!

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Where to start?

Pay-to-play integrated solutions

BaseSpace(Illumina) and MANY-MANY more!

CLC Genomics

Workbench

(QIAGEN)

Genomatix Genome

Analyzer (genomatix)

NextGENe(Softgenetics)

Pros:

• All-in-one multi-application packages

• Start-to-end pre-made pipelines for some

generic analyses

Cons:

• Cost, can be very expensive

• Not flexible

usegalaxy.org

galaxyproject.org/public-galaxy-servers/

More than 80 publicly accessible Galaxy servers

Galaxy platform

• Free to use.

• No need for programming experience.

• Integrates many bioinformatics tools within one interface.

• Keeps track of all the steps performed in analysis.

• Data is not overwritten.

• Even if you delete the datasets, the history keeps the tools used.

• Can create workflow to repeat an analysis.

• Pre-uploaded reference genomes.

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usegalaxy.org

Galaxy platform

• Register

• Tutorials – Galaxy 101, Interactive tools, etc.

• Great video library

• Sign-up for news, webinars, etc.

usegalaxy.org

Galaxy platform

• Many useful Tools for NGS analysis and other

• Main Window shows info, details, results, etc.

• History helps to keep track of every step

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Galaxy platform – RNA-seq pipeline

usegalaxy.org

• FASTQ file(s)

• reference genome

• GFF/GTF gene annotation file

Galaxy platform – RNA-seq pipeline

usegalaxy.org

• FASTQ file(s)

• reference genome

• GFF/GTF gene annotation file

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Galaxy platform – RNA-seq pipeline

usegalaxy.org

Galaxy platform – RNA-seq pipeline

usegalaxy.orgThere are many more tools to use!

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Many other pipelines

usegalaxy.org

galaxyproject.org/public-galaxy-servers/

More than 80 publicly accessible Galaxy servers

Galaxy platform

• Free to use.

• No need for programming experience.

• Integrates many bioinformatics tools within one interface.

• Keeps track of all the steps performed in analysis.

• Data is not overwritten.

• Even if you delete the datasets, the history keeps the tools used.

• Can create workflow to repeat an analysis.

• Pre-uploaded reference genomes.