Bowtie can quickly align large sets of short DNA sequences to large genomes.
You can use Bowtie 2 to align reads of about 50 to 100s or 1,000s of characters. For human genome, the memory footprint is approximately 3.2 GB.
Bowtie 2 forms the basis for other tools like Tophat, a fast splice junction mapper for RNA-seq reads, and Cufflinks, a tool for transcriptome assembly and isoform quantitation from RNA-seq reads.
For more information, see http://bowtie-bio.sourceforge.net/bowtie2/index.shtml.
RNA-Seq Alignment v1.0 Online Help