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
Assembly For Double-Ended Short-Read Sequencing Technologies: J. Chen, S. Skiena, Advances in Genome Sequencing Technology and Algorithms, 2007.
Crystallizing short-read assemblies around seeds: Mohammad Sajjad Hossain, Navid Azimi, Steven Skiena, The Seventh Asia Pacific Bioinformatics Conference (APBC), January 2009.
Our 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.
SHORTY in the press
Moving From Simulations to Real Data, Short-Read Assemblers Start Facing Off
New Algorithms Indicate That 'Microread' Genome Assembly May Be Within Reach
Related Projects/Publications/Links
List of a lot of useful projects
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Velvet: Algorithms for De Novo Short Read Assembly Using De Bruijn Graphs
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer