@article {38553, title = {Ultrafast and memory-efficient alignment of short DNA sequences to the human genome}, journal = {Genome BiologyGenome Biology}, volume = {10}, year = {2009}, type = {10.1186/gb-2009-10-3-r25}, abstract = {Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.}, isbn = {1465-6906}, author = {Langmead, Ben and Trapnell, Cole and M. Pop and Salzberg, Steven L.} }