TY - JOUR AU - Langmead, Ben AU - Trapnell, Cole AU - Pop, Mihai AU - Salzberg, Steven L. PY - 2009 DA - 2009/03/04 TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biology SP - R25 VL - 10 IS - 3 AB - 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. SN - 1474-760X UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER -