Canadian Bioinformatics Workshops

2Module #: Title of Module

Module 4 Genome Visualization

Module 4 bioinformatics.ca History of Genome Visualization 1800s 1900s 2000s time

Module 4 bioinformatics.ca Why is visualization important? make large amounts of data more interpretable glean patterns from the data sanity check / visual debugging more…

Module 4 bioinformatics.ca Lecture Outline Part I:Genome Browsing Part II:Savant Genome Browser Part III:Future of Genome Visualization

GENOME BROWSERS

Module 4 bioinformatics.ca What is a “Genome Browser” linear representation of a genome position-based annotations, each called a track – continuous annotations: e.g. conservation – interval annotations: e.g. gene, read alignment – point annotations: e.g. SNPs user specifies a subsection of genome to look at

Module 4 bioinformatics.ca Rough comparison of Genome Browsers UCSCEnsemblGBrowseSavantIGV ModelServer Client Interactive HTS support Database of tracks Plugins No supportSome supportGood support

Module 4 bioinformatics.ca Server-side model (e.g. UCSC, Ensembl, Gbrowse) central data store renders images sends to client server client requests images displays images

Module 4 bioinformatics.ca Client-side model (e.g. Savant, IGV) stores data server client local HTS store renders images displays images HTS machine

Module 4 bioinformatics.ca Limitations of all genome browsers do not support multiple genomes simultaneously do not capture 3-dimensional conformation do not capture spatial or temporal information do not integrate well with analytics cannot be customized – e.g. with new visualizations, datasources, etc. most main design goal of Savant

Module 4 bioinformatics.ca Other genome visualizations circular hive

SAVANT GENOME BROWSER

Module 4 bioinformatics.ca Motivation 1: Sequencing Revolution sequencing data is generated in huge volumes server-side browsers not designed for huge volumes of data UCSC genome browser published

Module 4 bioinformatics.ca Motivation 2: Need for visual analytics Q: how to analyze all this data? A: multi-step computational pipelines large disconnect between computation and visualization Sequence Illumina, AB, etc. Alignment MOSAIK, SHRiMP, etc. Analysis command-line SNP, indel, CNV caller, etc. Formatting ad-hoc file parsing Visualization UCSC, Ensembl, Gbrowse, IGV, etc.

Module 4 bioinformatics.ca Savant Genome Browser platform for integrated visual analysis of genomic data feature-rich genome browser client-side model extendable via plugin framework

Module 4 bioinformatics.ca revamped interface programmable Genome Browser Revolution

Module 4 bioinformatics.ca Who uses Savant? downloaded over 1,000 times in 70 countries used for wet-lab validation, algorithm development, diagnostics, more

Module 4 bioinformatics.ca Very short list of features Data Format Support FASTA, BED, WIG, GFF, tab-delimited, BAM local and remote Alternative Visualization Modes pack, squish for BED and GFF tracks mismatch, SNP, matepair modes for BAM tracks Speed and Interactivity very fast data access (<1s) small memory footprint (<250 MB) Extras programmable via plugin framework, sessions, bookmarking of interesting regions, track locking, data selection System Requirements ~ none, works on all major operating systems

Module 4 bioinformatics.ca Video Demonstration of Features visit savantbrowser.com to rewatch

Module 4 bioinformatics.ca Plugin Development plugin development is easy – API contains over a hundred prebuilt functions SDK includes API, example plugin project, step-by-step tutorial connectvisualizeanalyze

Module 4 bioinformatics.ca Savant Summary Savant is a platform for integrated visualization and analysis of genomic data stand-alone genome browser novel features: e.g. table view, visualization modes, data selection, etc. extensible through plugin framework makes interpretation and analysis of genomic data easier and more efficient

FUTURE OF GENOME VISUALIZATION

Module 4 bioinformatics.ca Genome Visualization Wishlist move away from reference-centric browsing capture spatial and temporal information capture 3-dimensional information browse by biological function, rather than by coordinates … send your wishlist to

Module 4 bioinformatics.ca We are on a Coffee Break & Networking Session