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bowtie website  

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. 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).

Bowtie is a part of the Tuxedo suite.


If you are using bowtie we installed you do not need to specify the path, only the database name. If you are using some other software and must specify the full path use '/data/reference/bowtie'

If you have additional indexes that could be of use to others in the UF community please contact us and we'll add them to the reference file space. You can, of course build your own indexes for your own use, simply pass the path to those indexes in the bowtie command.

We provide both Bowtie and Bowtie2.

Required Modules

modules documentation


  • bowtie -loads the default Bowtie version

System Variables

  • HPC_BOWTIE_DIR - installation directory
  • HPC_BOWTIE_BIN - executable directory
  • HPC_BOWTIE_DOC - documents directory
  • HPC_BOWTIE_EX - examples directory
  • HPC_BOWTIE_SCR - scripts directory
  • BOWTIE_INDEXES - pre-built index files directory

Additional Information

Note: If your data is compressed your job script should add another CPU core to the job resource request to accommodate the external gzip process that bowtie will run.