Cassava genome hub

Cassava Genome HubUpdates on cassava genomics big data management and analysis.

Anestis Gkanogiannis

CIRAD

June 24, 2016

IntroductionBig Data

The Cassava Genome HubUsecase

Table of Contents

1 Introduction2 Big Data3 The Cassava Genome Hub

ArchitectureTechnologiesData

ToolsJBrowseSNiPlayGIGWADiffExDBGenetic MapQuerying ToolsGalaxy

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Who am I?

Born and raised in the Greek island of Evia.

Physicist, 1998 - 2003, BSc, UOC, Crete, Greece

Informatician

2003 -2005, MSc in Information Retrieval, AUEB, Athens2005 - 2011, PhD in Machine Learning, AUEB, Athens

2011 - 2013, Text Analysis, UNB, Fredericton, Canada

2013 - 2015, Bacterial Genomics, Genoscope, Paris,France

2015 - 2016, Plant Genomics, CIRAD, Montpellier, France

2016 - ??



Who are we?



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Definition

Everyone is talking about it.

Any combination of Very hot subject in Omics.



Definition

Everyone is talking about it. Any combination of

Very hot subject in Omics.



Definition

Everyone is talking about it. Any combination of Very hot subject in Omics.



ArchitectureTools

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ArchitectureTools

http://www.cassavagenome.org



ArchitectureTools

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ArchitectureTools



ArchitectureTools

Technologies



ArchitectureTools

Data

VolumeTens of TB of raw sequence data.

Hundreds of GB of processed and analyzed data.

Velocity

New and improved assemblies and annotation.

New sequencing technologies and lower cost.

Variety

Genomic sequences, RNASeq,RADSeq, etc.

Annotation

Variants

Metabolomic



ArchitectureTools

Data

Public/Private Type Technology Description Publication Samples

Public Genomic WGS Assembly and annotation V6 Prochnik et al, 2012Public Genomic WGS Genetic Variants Bredeson et al, 2016 61Private Genomic RADSeq Genetic Variants in progress 1100Private Genomic WGS Genetic Variants in progress 34Public Transcriptomic RNASeq Response to Xanthomonas Munoz-Bodnar et al, 2014 12(2*6)Public Transcriptomic RNASeq Response to Xanthomonas Cohn et al, 2014 18(3*6)Private Transcriptomic RNASeq Response to White Fly in progress 16(2*8)

Table: Resources of data available



ArchitectureTools

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ArchitectureTools

JBrowse

A fast, embeddableGenome Browser builtcompletely withJavaScript and HTML5.



ArchitectureTools

SNiPlay

SNiPlay3: a web-basedapplication forexploration and largescale analyses of genomicvariations.



ArchitectureTools

GIGWA

A web-based tool thatprovides an easy andintuitive way to explorelarge amounts ofgenotyping data byfiltering it.

Data storage relies onMongoDB, which offersgood scalabilityproperties.

Can handle multipledatabases and may bedeployed in either single-or multi-user mode, whileit provides a wide rangeof popular exportformats.



ArchitectureTools

DiffExDB

Explore differentialexpression analyses.Visualize heatmap ofRPKM expression values.



ArchitectureTools

CMap

A browser-based tool forthe visual comparison ofvarious maps (sequence,genetic, etc.).



ArchitectureTools

QuigMap

A fast cross-platformgenetic map viewer.



ArchitectureTools

BLAST

blastn : Searchnucleotide databasesusing a nucleotide query.

blastp : Search proteindatabases using a proteinquery.

blastx, tblastn, tblastx



ArchitectureTools

Advanced Search

Search for genomicfeatures, genomiclocations, enzymaticcodes, gene ontologyterms, etc.

Output as nucleotide ortranslated aminoacidsequences.



ArchitectureTools

Pathway Tools

Creates a newPathway/GenomeDatabase (PGDB)containing the predictedmetabolic pathways.

Supports query,visualization, and analysisof PGDBs.



ArchitectureTools

Galaxy

A scientific workflow,data integration and dataanalysis platform thataims to makecomputational biologyaccessible to researchscientists that do nothave computerprogramming experience.

Provides means to buildmulti-step computationalanalyses. It provides agraphical user interfacefor specifying what datato operate on, what stepsto take, and what orderto do them in.



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Thank you!

Cassava genome hub

Science

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