Bowtie 2

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