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Bowtie
Bowtie is an ultrafast, memory-efficient aligner designed to quickly align large sets of short reads to large genomes. Bowtie indexes the genome to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB for single-read alignment or 2.9 GB for paired-end alignment. Multiple processors can be used simultaneously to achieve greater alignment speed.
Bowtie 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/index.shtml.