Align sequence reads to reference sequences using the Bowtie 1 (bowtie) and Bowtie 2 (bowtie2) alignment functions. Bowtie 1 is geared toward aligning relatively short reads (up to 50 bp). Bowtie 2 is more suitable for reads longer than 50 bp and provides several benefits including single- and paired-end reads support, local and end-to-end alignment support, and gapped alignment with affine penalties.