New sequencing technologies, such as Roche 454, ABI SOLiD and Illumina Solexa, have been increasingly developed at an astounding pace with advantages of reduced time, costs, and efforts. To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, a sophisticated software MagicViewer is developed to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design.

Highlights of MagicViewer:

• End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization
• Automatically generate publication-quality lollipop diagrams (show example)
• Integrated 1-click multiple sequence alignment
• Automated CpG highlighting- never spend your time highlighting CpGs by hand anymore
• Open electropherogram files to check for sequencing problems (requires an electropherogram viewer such as Chromas LITE)
• Generate MethDB-compatible DNA methylation files for database submission
• Factor 5 speedup of sequence analysis while at the same time achieving better data quality

Intended users:

• Anyone who works with DNA methylation data from bisulfite sequencing
• Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work)

A typical screenshot of MagicViewer: