bowtie2 v2.2.6

Bowtie 2 is described as 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. 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.

The website asks:

Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

Accessing the software

To load the module:

$ module load apps/bowtie2/v2.2.6

An example command to include in your job script:

bowtie2 --threads <NumCores> \
      -x $BOWTIE2_EXAMPLES/index/lambda_virus \
      -U $BOWTIE2_EXAMPLES/reads/reads_1.fq \
      -S <SAM file>

The installation root for this application can be found at ${BOWTIE2_ROOT} and examples can be found at ${BOWTIE2_EXAMPLES} when the module is loaded into the environment.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the Bowtie 2 website for more information regarding this application.

Last modified: 7 October 2017