FAAST: Flow-space Assisted Alignment Search Tool
1 IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83 Linköping, Sweden
2 Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, S-171 77 Stockholm, Sweden
BMC Bioinformatics 2011, 12:293 doi:10.1186/1471-2105-12-293Published: 19 July 2011
High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments.
We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool).
We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed.