Computational Biology Lab, Simon Fraser University
Computer Architecture Lab (CALCM), Carnegie Mellon University.
Alkan Lab, Bilkent University
sirFAST is designed to map short reads generated with the Compelete Genomics (CG) platform to reference genome assemblies; in a fast and memory-efficient manner.
Currently Supported Features:
- Output in SAM format
- Support Hamming distance
- Paired-end mapping
- Edit distance (Indels)
git clone https://github.com/fhormoz/sirFAST.git
- New semi-cache-oblivious algorithm to improve mapping speed.
- SAM format output.
Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Onur Mutlu, and Can Alkan,
"Fast and Accurate Mapping of Complete Genomics Reads" Methods, October 22, 2014. PDF