Bowtie¶

Bowtie and Bowtie 2 are tools for aligning sequencing reads to long reference sequences. The bowtie bundle has two variants one for version 1.3.1 and one for version 2.5.1.

UFS HPC Usage Example¶

Bowtie 2 is the default variant and can be used by running the following command the terminal:

1	`module load bowtie`

Add release=1 to the previous command to use Bowtie:

module load bowtie release=1

Once the variant is loaded the Bowtie commands can be run as shown below, first example is for Bowtie and the second example is for Bowtie 2:

bowtie
bowtie-align-s
bowtie-build-l
bowtie-inspect
bowtie-inspect-s
bowtie-align-l
bowtie-build
bowtie-build-s
bowtie-inspect-l

bowtie2
bowtie2-align-s
bowtie2-build-l
bowtie2-inspect
bowtie2-inspect-s
bowtie2-align-l
bowtie2-build
bowtie2-build-s
bowtie2-inspect-l

The bowtie_shell command can be run for a shell in the bowtie bundle.

1	`bowtie_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

Bowtie¶

Bowtie 2¶

Licensing Information¶

Bowtie is licensed under the Artistic License 2.0, while Bowtie 2 is licensed under the GPLv3 license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za