From the Bowtie2 Home Page: Bowtie 2 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. 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.



Authorized Users

  • CIRCE account holders
  • SC account holders


  • CIRCE cluster
  • SC cluster


  • apps/bowtie/

Running Bowtie2 on CIRCE/SC

The Bowtie2 user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

Notable flags:

-p N , will set the number of tasks to use, where N is the number of tasks

#SBATCH --job-name=test_bowtie2
#SBATCH --time=04:00:00
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=2096
#SBATCH -o output.%j.%N.txt
#SBATCH -e error.%j.%N.txt

#### SLURM single node bowtie2 test
#### to run for 4 hours
#### using 4 processing cores and 8GB of memory

# Unload all modules, then load the bowtie2 module:
module purge
module load apps/bowtie/

#always run in WORK when running batch jobs
mkdir $WORK/bowtie
cp $HOME/featureCounts_ex/*fa $WORK/bowtie
cp $HOME/featureCounts_ex/*fa* $WORK/bowtie
cp $HOME/trim_ex/SRR6202537_1.fastq $WORK/bowtie
cp $HOME/trim_ex/SRR6202537_2.fastq $WORK/bowtie
cd $WORK/bowtie

#computation steps

bowtie2-build --threads 4 hg38.fa hg38
bowtie2 -p 4 -x hg38 -1 SRR6202537_1.fastq -2 SRR6202537_2.fastq -S SRR6202537.sam --no-unal

cp *.sam $HOME/bowtie_ex

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./
  • You can view the status of your job with the “squeue -u <username>” command


Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • Bowtie2 Examples
    • /apps/bowtie/

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Bowtie2 to the IT Help Desk: