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


BACKGROUND
CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/


BACKGROUND
liangc@muohio.edu or  liangc.mu@gmail.com; glji@xmu.edu.cn


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
Pei
P
Li
Guoli
G
Ji
Min
M
Dong
Emily
E
Schmidt
Douglas
D
Lenox
Liangliang
L
Chen
Qi
Q
Liu
Lin
L
Liu
Jie
J
Zhang
Chun
C
Liang
D003196:Computer Graphics; D020451:Contig Mapping; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D017422:Sequence Analysis, DNA; D012984:Software