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Running Galaxy in AnVIL

Natalie Kucher

AnVIL Demos

August 31, 2023

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Terms of Use

Except where otherwise indicated, The contents of this slide presentation are available for use under the Creative Commons Attribution 4.0 license.

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You are free to adapt and share the work, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.

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Sample attribution: [Title of work] by Johns Hopkins Data Science Lab. CC-BY 4.0

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Learning Objectives

  1. Learn how to launch Galaxy in AnVIL and import data
  2. Understand how to find, import, and run workflows
  3. Visualize a sample variant using JBrowse
  4. Learn how to save your history back to AnVIL
  5. Show how to shut down Galaxy in AnVIL

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Overview

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What is Galaxy?

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What is Galaxy?

Analyze

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What is Galaxy?

Interact

Analyze

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What is Galaxy?

Scale

Analyze

Interact

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What is Galaxy?

Share

Scale

Analyze

Interact

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Production Scale Workflows

https://dockstore.org/search?descriptorType=gxformat2&organization=iwc-workflows&entryType=workflows&searchMode=files

https://galaxyproject.org/projects/vgp/workflows/

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Activity

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SARS-CoV-2 Variants

November

2021

https://covid.cdc.gov/covid-data-tracker/?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Fcases-updates%2Fvariant-proportions.html#variant-proportions

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Raw Data

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https://anvil.terra.bio/#workspaces/gdscn-exercises/SARS-CoV-2-Genome/data

Raw data

Collected by Virginia Commonwealth University published November 2021

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Quality Check

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Raw data

Quality check

https://anvilproject.org/

FastQC

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Alignments

3’- A G C T T A C A G C G C C C A G T C -5’

3’- A G C T T A C A G C G C C C A G T C -5’

3’- A G C T T A C A G C G C C C A G T C -5’

3’- A G C T T A C A G C G C C C A G T C -5’

3’- A G C T T A C A G T G C C C A G T C -5’

3’- A G C T T A C A G C G C C C A G T C -5’

Reference

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Read

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Read

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Read

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Read

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Read

Raw data

Quality check

Alignment

FastQC

BWA-MEM

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Variant Visualization

Raw data

Quality check

Alignment

FastQC

DISCOVERY!

BWA-MEM

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Enable workflows with Galaxy

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Enable Workflows with Galaxy Exercises

  • Clone SARS-CoV-2-Genome Workspace
  • Launch Galaxy
  • Import Data
  • Find Workflows
  • Run Workflow
  • Explore Results
  • Export History
  • Shut Down

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Enable Workflows with Galaxy Exercises

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Contributions

  • Katherine Cox
  • Ava Hoffman
  • Elizabeth Humphries
  • Natalie Kucher
  • Robert Meller
  • Stephen Mosher
  • Frederick Tan

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