Deprecated: Use of this version of Bowtie2 is deprecated. More information on our Applications Support and Retention Policy.

There is a newer install of Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Accessing Bowtie2

To load the module for Bowtie2 please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load Bowtie2/

BEAR Apps Version




The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Bowtie2 and Python

The bowtie2-build and bowtie2-inspect scripts require Python. Please load either Python 3 or Python 2, as necessary, if you wish to use these scripts.

More Information

For more information visit the Bowtie2 website.


This version of Bowtie2 has a direct dependency on: foss/2018b tbb/2018_U5-GCCcore-7.3.0 zlib/1.2.11-GCCcore-7.3.0

Required By

This version of Bowtie2 is a direct dependent of: ariba/2.13.5-foss-2018b-Python-3.6.6 srst2/0.2.0-foss-2018b-Python-2.7.15 TRAPeS/e65bb7b-foss-2018b-Python-2.7.15 Trinity/2.8.4-foss-2018b

Other Versions

These versions of Bowtie2 are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 3rd June 2019