CBrowse – a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis

CBrowse is an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard 3-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/.

  • Li P, Ji G, Dong M, Schmidt E, Lenox D, Chen L, Liu Q, Liu L, Zhang J, Liang C. (2012) CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics [Epub ahead of print]. [abstract]