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

文献类型： 外文期刊

第一作者： Li, Pei

作者： Li, Pei;Ji, Guoli;Dong, Min;Chen, Liangliang;Liu, Qi;Li, Pei;Dong, Min;Schmidt, Emily;Lenox, Douglas;Liu, Lin;Liang, Chun;Schmidt, Emily;Lenox, Douglas;Liang, Chun;Zhang, Jie;Liang, Chun

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期刊名称：BIOINFORMATICS （ 影响因子：6.937； 五年影响因子：8.47 ）

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收录情况： SCI

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.

分类号： Q81

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