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Bioinformatics. 2012 Sep 15;28(18):2382-4. doi: 10.1093/bioinformatics/bts443. Epub 2012 Jul 12.

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

Author information

  • 1Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.

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.cn

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
22789590
[PubMed - indexed for MEDLINE]
PMCID:
PMC3436847
Free PMC Article
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