facs README

For more information, please visit the FACS website:
http://facs.scilifelab.se

Overview

New generation sequence technologies and the sequencing of increasingly
complex datasets demand new efficient and specialized sequence analysis
algorithms. Often, it is only the 'novel' sequences in a complex dataset that
are of interest and the superfluous sequences need to be removed. A novel
algorithm, FACS (Fast and Accurate Classification of Sequences), is introduced
that can accurately and rapidly align sequences to a reference sequence. FACS
was first optimized and validated using a synthetic metagenome dataset. An
experimental metagenome dataset was then used to show that FACS is at least
three times faster and more accurate than BLAT and SSAHA2 in classifying
sequences when using references larger than 50Mbp.

Citation

Reference:
Henrik Stranneheim, Max Käller, Tobias Allander, Björn Andersson,
Lars Arvestad, Joakim Lundeberg. Classification of DNA sequences using Bloom
filters. Bioinformatics, 2010 July 1; 26(13):1595-1600.

Published online 2010 May 13. http://dx.doi.org/doi:10.1093/bioinformatics/btq230

Contact

Henrik Stranneheim <henrik.stranneheim@scilifelab.se>
Lars Arvestad <arve+facs@csc.kth.se>