Genomic visualisation at TGAC

Genomic Visualisations at TGAC

Anil ThankiAnil.Thanki@tgac.ac.uk@anilthanki

Tools and Resources

http://www.tgac.ac.uk/tools-resources/

htttps://github.com/TGAC/

Tools and Resources

TGAC Browser

TGAC Browser is an open-source genome browser developed to visalise genomic annotations from Ensembl core database and NGS data.

TGAC Browser is an open-source genome browser developed to visalise genomic annotations from Ensembl core database and NGS data.

TGAC Browser server-client

ServerServer

ClientClient

EnsemblCore

database

EnsemblCore

database

Java SQL DAO

Java SQL DAO

Java ClassesJava

Classes

Cache

Cache

Session files

Session files

User files

User files

Ajax

JSON

Java-genomics-IO

Java-genomics-IO

JavaScriptJavaScript CSSCSS

JSPJSP SVGSVG

HTMLHTML

Supported Data

Ensembl Data

• Genomic features from Ensembl Database• Genes, alignments, SNPs, repeats, assembly, markers, etc

• Genomic features from Ensembl Database• Genes, alignments, SNPs, repeats, assembly, markers, etc

BAM/SAM and wig/bigwig

Visualising reads directly from SAM/BAM fileVisualising reads directly from SAM/BAM file

Visualising expression data directly from wig/bigwig fileVisualising expression data directly from wig/bigwig file

VCF and GFF

• Visualising variant data directly from VCF file• Coloured based on base pairs

• Insertion, deletion, mutation

• Visualising variant data directly from VCF file• Coloured based on base pairs

• Insertion, deletion, mutation

Visualising genes data directly from GFF file•Exons, Introns, CDS

Visualising genes data directly from GFF file•Exons, Introns, CDS

Visual types

Individual featureIndividual feature

Overview with bar chartOverview with bar chart

Overview with heatmapOverview with heatmap

BLAST Integration

Java classesJava classes

BLASTManager db

BLASTManager db

NCBINCBI Local machineLocal

machineHPC clusterHPC

cluster

FilesFilesAnalysis Daemon

Analysis Daemon

TGAC BrowserTGAC Browser

BLAST Integration

BLAST results for sequence search with BLAST history logsBLAST results for sequence search with BLAST history logs

BLAST Integration

BLAST results showing as a track run from a genomic feature with coloured with scoring system and indel information

BLAST results showing as a track run from a genomic feature with coloured with scoring system and indel information

Manual Annotation

Read Only Read and Write

Manual Annotation

Read Only Read and Write

ManAnn db

Curator

Manual Annotation

Edit various genomic track credentialsEdit various genomic track credentials

TGAC Browser

TGAC Browsers

TGAC Browsers

compara

Aequatus Browser

compara

Aequatus Browser

Aequatus browser is a graphical interface to visualise homologous information of related genes.

Aequatus browser is a graphical interface to visualise homologous information of related genes.

Aequatus Browser

Controls

Search GenomesChromosomes

Navigation PanelGene Members

Homologous View

Aequatus Browser

e!Genome1

e!Genome1

e!Genome2

e!Genome2

e!Genome3

e!Genome3

e! COMPARA

e! COMPARA

Aequatus Browser

e!Genome1

e!Genome1

e!Genome2

e!Genome2

e!Genome3

e!Genome3

e! COMPARA

e! COMPARA

Aequatus Browser

e!Genome1

e!Genome1

e!Genome2

e!Genome2

e!Genome3

e!Genome3

e! COMPARA

e! COMPARA

Aequatus Browser

e! Compara stores multiple sequence alignment as CIGAR line

Insertions

Deletions

Aequatus Browser

oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]

Default View

Aequatus Browser

oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]

Legends

Aequatus Browser

oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]

Visual settings

Aequatus Browser

oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]

Visual settings

Aequatus Browser

oxytocin/neurophysin I prepropeptide [Source:HGNC Symbol;Acc:8528]

Search

Aequatus Browser

Releasing ũnus (1st) version of code to GitHub soon

htttps://github.com/TGAC/Aequatus-Browser

Acknowledgements

• Robert Davey• Xingdong Bian• Sarah Ayling• Mario Caccamo• Jon Wright• Gemy Kaithakottil• Daniel Mapleson• Martin Ayling• Chris Bennett

• Jinhong Li• JIC

• Mariella Ferrante• Remo Sanges

• SZN, Italy• Paul Linehan

• Ireland• Burkhard Steuernagel

• TSL

http://tgac-browser.tgac.ac.ukhttp://tgac-browser.tgac.ac.uk/aequatus-browser

tgac.browser@tgac.ac.uk @anilthanki and @tgacbrowser