Shorty Assembler

Download Shorty2.0 (modified version) With new Enhancements.

SHORTY - A New de novo Assembler

With the advent of next generation short read sequencing technologies, the old problem of sequence assembly has re-emerged. The new technologies not only have ultra high throughput, but also reduce the length of reads drastically in comparison to traditional Sanger type sequencing. These technologies also suffer from higher margin of sequencing errors and other artifacts. We started developing an assembler from scratch to address all these issues. Our assembler SHORTY is targetted for de novo assembly of microreads with mate pair information and sequencing errors. SHORTY has some novel approach and features in addressing the short read assembly problem. To learn more about SHORTY, visit the links in the next section.

Papers On SHORTY

1. Assembly For Double-Ended Short-Read Sequencing Technologies: J. Chen, S. Skiena, Advances in Genome Sequencing Technology and Algorithms, 2007.

2. Crystallizing short-read assemblies around seeds: Mohammad Sajjad Hossain, Navid Azimi, Steven Skiena, The Seventh Asia Pacific Bioinformatics Conference (APBC), January 2009.

3. ISMB 2008 poster abstract.

Getting SHORTY

SHORTY is going through constant development and improvement. Though it is meant to work for any platform of short read sequencing, currently we are more focused on ABI's SOLiD type data. This release is more ABI friendly.