Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long, e.g. mammalian, genomes. Bowtie 2 indexes the genome with an FM Index, based on the Burrows-Wheeler Transform or BWT, to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie 2 outputs alignments in SAM format, enabling interoperation with a large number of other tools, e.g., SAMtools, GATK, that use SAM. Bowtie 2 is distributed under the GPLv3 license, and it runs on the command line under Windows, Mac OS X and Linux.
Bowtie 2 is often the first step in pipelines for comparative genomics, including for variation calling, ChIP-seq, RNA-seq, BS-seq. Bowtie 2 and Bowtie, also called "Bowtie 1" here, are also tightly integrated into some tools, including
TopHat: a fast splice junction mapper for RNA-seq reads,
Cufflinks: a tool for transcriptome assembly and isoform quantitiation from RNA-seq reads,
Crossbow: a cloud-enabled software tool for analyzing reseuqncing data, and
Myrna: a cloud-enabled software tool for aligning RNA-seq reads and measuring differential gene expression.
Bowtie is a prerequisite for tophat.
Bowtie 2 requests that you cite this paper for published research.