Syndicated from PubMed RSS Feeds
Savant: Genome Browser for High Throughput Sequencing Data.
Bioinformatics. 2010 Jun 20;
Authors: Fiume M, Williams V, Brudno M
MOTIVATION: The advent of High Throughput Sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictions and understand the functional effects, especially in the context of other datasets. RESULTS: We introduce Savant, the Sequence Annotation, Visualization and ANalysis Tool, a desktop visualization and analysis browser for genomic data. Savant was developed for visualizing and analyzing HTS data, with special care taken to enable dynamic visualization in the presence of gigabases of genomic reads and references the size of the human genome. Savant supports the visualization of genome-based sequence, point, interval, and continuous datasets, and multiple visualization modes that enable easy identification of genomic variants (including SNPs, structural, and copy-number variants), and functional genomic information (e.g. peaks in ChIP-seq data) in the context of genomic annotations. AVAILABILITY: Savant is freely available at http://compbio.cs.toronto.edu/savant CONTACT: [email protected].
PMID: 20562449 [PubMed - as supplied by publisher]
More...
Savant: Genome Browser for High Throughput Sequencing Data.
Bioinformatics. 2010 Jun 20;
Authors: Fiume M, Williams V, Brudno M
MOTIVATION: The advent of High Throughput Sequencing (HTS) technologies has made it affordable to sequence many individuals' genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictions and understand the functional effects, especially in the context of other datasets. RESULTS: We introduce Savant, the Sequence Annotation, Visualization and ANalysis Tool, a desktop visualization and analysis browser for genomic data. Savant was developed for visualizing and analyzing HTS data, with special care taken to enable dynamic visualization in the presence of gigabases of genomic reads and references the size of the human genome. Savant supports the visualization of genome-based sequence, point, interval, and continuous datasets, and multiple visualization modes that enable easy identification of genomic variants (including SNPs, structural, and copy-number variants), and functional genomic information (e.g. peaks in ChIP-seq data) in the context of genomic annotations. AVAILABILITY: Savant is freely available at http://compbio.cs.toronto.edu/savant CONTACT: [email protected].
PMID: 20562449 [PubMed - as supplied by publisher]
More...