PerM  Efficient mapping of short reads with periodic full sensitive spaced seeds

PerM is a great SOLiD reads mapping tool that you should try. In one of our recent test, PerM reaches 43 million reads per CPU hour, full sensitive to 3 mismatches and partial sensitive to 10 mismatches when mapping 50-bp SOLiD read to the whole hg18 and output in SAM format. PerM takes advantage of large memory and multiple CPU to build hg18 index in 35 min (16 CPU and 15 G memory).  It can also be full sensitivity for alignments within 4 mismatches and paritial sensitive to higher number mismatches. The input can be fasta, fastq, csfastq w/wo quality files, and the reference can be multiple chromosomes or transcriptom. Mapping can be done in one command. 

Visit our webpage at  http://code.google.com/p/perm/   for download and more information.

This tool was developed by Ting Chen's group, Center of Excellence in Genomic Sciences at the University of Southern California. Analysis of the algorithm is published at Bioinformatics journal.