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bowtie2 website  

Bowtie2 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, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie2 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. Bowtie2 supports gapped, local, and paired-end alignment modes.

Bowtie is a part of the Tuxedo suite.

If you are using bowtie or bowtie2 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/bowtie2. 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 as an argument to the bowtie2 command.

Required Modules

modules documentation


  • bowtie2 -loads the default Bowtie2 version

System Variables

  • HPC_BOWTIE2_DIR - installation directory
  • HPC_BOWTIE2_BIN - executable directory
  • HPC_BOWTIE2_DOC - documents directory
  • HPC_BOWTIE2_EX - examples directory
  • HPC_BOWTIE2_SCR - scripts directory
  • BOWTIE2_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.