RMAPQ was developed for Solexa reads.
TIP. The tool will guess the length of the reads, however, if you select to trim the reads, the Maximal Length of the Reads must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end.
What it does
This tool runs rmapq (for more information, please see the reference below), searching against a genome build with sequence qualities.
RMAP is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/