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

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

SUBMITTER: Li P 

PROVIDER: S-EPMC3436847 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature