CBrowse is a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. It takes the contig sequence file and its relevant SAM/BAM file as the input, processes the input data, detects polymorphisms and repeats, and generates image, JSON and MySQL-compatible text files that can be directly utilized by different viewers of CBrowse. There are 5 major viewers in CBrowse:
(1) Contig viewer presents summary information about the assembly as well as individual contig
(2) Sequence viewer allows users to examine and scan individual nucleotides of each contig
(3) Polymorphism Viewer provides the polymorphism types (SNPs, single indels, and other mismatches/indels), positions and frequencies of each contig
(4) SSR Viewer provides the detected simple sequence repeats (the unit size of 1-12 nt, either perfect or imperfect matches) in each contig
(5) Alignment Viewer offers both bird-eye and nucleotide resolutions of sequence alignments, with color-coded nucleotide differences between contigs and their component sequence reads
CBrowse (Contig Browser) is a generic tool for visualizing and analyzing transcriptome assembly and contigs. You can download the source code, process your own data, and depoly it as a web service in your computer server.
Pei Li, Guoli Ji, Min Dong, Emily Schmidt, Douglas Lenox, Liangliang Chen, Qi Liu, Lin Liu, Jie Zhang and Chun Liang (2012) CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics, doi: 10.1093/bioinformatics/bts443
CBrowse uses the external program Phobos for SSR detection. So, it is important for users to cite Phobos if CBrowse is used in their research work.
Although CBrowse is distributed under the GNU General Public License, Phobos is free only for academic users. A commercial license for Phobos can be obtained from the author.