  Summary: We present an extension of CUSHAW2 for fast and accurate alignments
of SOLiD color-space short-reads. Our extension introduces a double-seeding
approach to improve mapping sensitivity, by combining maximal exact match seeds
and variable-length seeds derived from local alignments. We have compared the
performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real
color-space mate-paired reads to the human genome. The results show that
CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and
BFAST at an order-of-magnitude faster speed and significantly smaller peak
resident memory size. Availability: CUSHAW2 and all simulated datasets are
available at http://cushaw2.sourceforge.net. Contact<EMAIL_ADDRESS><EMAIL_ADDRESS>