Bowtie and Bowtie 2

E-mail Print PDF

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour on a typical workstation with 2 GB of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

  • runs on the command line under Windows, Mac OS X, Linux, and Solaris
  • can run on a typical desktop computer with 2 GB of RAM
  • can use multiple processors for greater alignment speed
  • can output alignments in the standard SAM format allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers (default output is not in SAM format)
  • can align colorspace reads against a colorspace index
  • can align paired-end reads
  • Bowtie is not a general-purpose alignment tool like MUMmer, BLAST or Vmatch. Bowtie works best when aligning short reads to large genomes


Bowtie 2 is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Differences with bowtie

  • If reads are shorter than 50 bp, Bowtie 1 might give better results in terms of speed and sensitivity.
  • Bowtie 2 fully supports gapped alignment with affine gap penalties. Number of gaps and gap lengths are not restricted, except via the user-supplied scoring scheme. Bowtie 1 only finds ungapped alignments.
  • For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
  • Bowtie 2 supports a "local" alignment mode, which doesn't require that reads align end-to-end. This produces alignments that might be "trimmed" (or "soft clipped") at one or both extremes in a way that optimizes alignment score. Bowtie 2 also supports an "end-to-end" alignment mode which, like Bowtie 1, requires that the read align entirely.
  • There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
  • Bowtie 2 does away with Bowtie 1's notion of alignment "stratum". In Bowtie 2 all alignments lie along a continuous spectrum of alignment scores.
  • There is no longer a distinction between "end-to-end" and "Maq-like" modes as in Bowtie 1. There is just one scoring scheme, similar to Needleman-Wunsch and Smith-Waterman.
  • Bowtie 2's paired-end alignment mode is more flexible than Bowtie 1's. For example, for pairs that do not align in a paired fashion, it will attempt to find unpaired alignments for each mate.
  • Bowtie 2 does not align colorspace reads.


Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009;10(3):R25. doi:10.1186/gb-2009-10-3-r25.

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012;9(4):357-359. doi:10.1038/nmeth.1923.




You are here: Software HTP-Sequencing Non Categorised Bowtie and Bowtie 2