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	CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
	Li, Pei ; Ji, Guoli ; Ji GL(吉国力) ; Dong, Min ; Schmidt, Emily ; Lenox, Douglas ; Chen, Liangliang ; Liu, Qi ; Liu, Lin ; Zhang, Jie ; Liang, Chun
	2012-09-15
关键词	GENOME BROWSER ANNOTATION MAP
英文摘要	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.; NIH-AREA [1R15GM94732-1 A1]; Key Project of Chinese National Programs for Fundamental Research and Development (973 Program) [2009CB118902]; National Natural Science Foundation of China [61174161]; Specialized Research Fund for the Doctoral Program of Higher Education of China [20090121110022]; Fundamental Research Funds for the Central Universities in China (Xiamen University) [2011121047, 201112G018, CXB2011035]
语种	英语
出版者	OXFORD UNIV PRESS
内容类型	期刊论文
源URL	[http://dx.doi.org/10.1093/bioinformatics/bts443]
专题	信息技术－已发表论文
推荐引用方式 GB/T 7714	Li, Pei,Ji, Guoli,Ji GL,et al. CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis[J],2012.
APA	Li, Pei.,Ji, Guoli.,吉国力.,Dong, Min.,Schmidt, Emily.,...&Liang, Chun.(2012).CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis..
MLA	Li, Pei,et al."CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis".(2012).

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