Introduction

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.CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cnSupplementary data are available at Bioinformatics online.

Publications

  1. CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
    Cite this
    Li P, Ji G, Dong M, Schmidt E, Lenox D, Chen L, Liu Q, Liu L, Zhang J, Liang C, 2012-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Pei Li
    Developer

    Department of Automation, Xiamen University, United States of America

  2. Guoli Ji
    Developer

  3. Min Dong
    Developer

  4. Emily Schmidt
    Developer

  5. Douglas Lenox
    Developer

  6. Liangliang Chen
    Developer

  7. Qi Liu
    Developer

  8. Lin Liu
    Developer

  9. Jie Zhang
    Developer

  10. Chun Liang
    Investigator

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Summary
AccessionBT000513
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByChun Liang