Dataset Information
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Ontology highlight
ABSTRACT: Summary
To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects.Availability
CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/Contact
liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cnSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Li P
PROVIDER: S-EPMC3436847 | biostudies-literature | 2012 Sep
REPOSITORIES: biostudies-literature
Publications
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Bioinformatics (Oxford, England) 20120712 18
<h4>Summary</h4>To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visual ...[more]
