Savant Genome Browser 2: visualization and analysis for population-scale genomics.

TitleSavant Genome Browser 2: visualization and analysis for population-scale genomics.
Publication TypeJournal Article
Year of Publication2012
AuthorsFiume, M., E. J. M. Smith, A. Brook, D. Strbenac, B. Turner, A. M. Mezlini, M. D. Robinson, S. J. Wodak, and M. Brudno
JournalNucleic Acids Res
Volume40
IssueWeb Server issue
PaginationW615-21
Date Published2012 Jul
ISSN1362-4962
KeywordsComputer Graphics, Genomics, High-Throughput Nucleotide Sequencing, INDEL Mutation, Internet, Polymorphism, Single Nucleotide, Population, Software
Abstract

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

DOI10.1093/nar/gks427
Alternate JournalNucleic Acids Res.
PubMed ID22638571
PubMed Central IDPMC3394255
Grant List / / Canadian Institutes of Health Research / Canada