Bowtie 2

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.

Interactive usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

The latest version of Bowtie 2 (currently version 2.3.4.2) is made available with the command:

$ module load Bowtie2/2.3.4.2-foss-2018b

After this any of the Bowtie 2 commands can be run from the terminal prompt. The available commands can be obtained using:

$ bowtie2 --help

Batch usage

The following is an example batch submission script, my_job.sh, to run the executable bowtie2-build with input files from the Bowtie2 example directory. The script requests 1 core using the OpenMP parallel environment smp with a runtime of 10 minutes and 4 GB of real memory to build a small and a large Bowtie index from a set of DNA sequences.

#!/bin/bash
#SBATCH --job-name=BOWTIE2_smp_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4000
#SBATCH --output=output_BOWTIE2_smp_1
#SBATCH --time=00:10:00
#SBATCH --mail-user=a.person@sheffield.ac.uk
#SBATCH --mail-type=ALL
module load Bowtie2/2.3.4.2-foss-2018b
bowtie2-build $EBROOTBOWTIE2/example/reference/lambda_virus.fa ./lambda_virus
bowtie2-build --large-index $EBROOTBOWTIE2/example/reference/lambda_virus.fa ./lambda_virus

The job is submitted to the queue by typing:

$ sbatch my_job.sh

Installation notes

Installation method

Bowtie 2 version 2.3.4.2 was installed using Easybuild 4.4.0, build details can be found in /usr/local/packages/live/eb/Bowtie2/2.3.4.2-foss-2018b/easybuild/

Testing

Testing has been conducted by running the small and a large Bowtie index build process as detailed in the batch job above.

The bowtie2-build cmds will output a set of 6 files with suffixes .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2. In the case of a large index these suffixes will have a bt2l termination. e.g.

[a_person@bessemer-node001 bowtie2test]$ bowtie2-build --large-index $EBROOTBOWTIE2/example/reference/lambda_virus.fa ./lambda_virus
[a_person@bessemer-node001 bowtie2test]$ bowtie2-build $EBROOTBOWTIE2/example/reference/lambda_virus.fa ./lambda_virus
[a_person@bessemer-node001 bowtie2test]$ ls -al
total 24896
-rw-r--r--  1 a_person a_group 4210730 Jan  4 16:01 lambda_virus.1.bt2
-rw-r--r--  1 a_person a_group 8405234 Jan  4 16:01 lambda_virus.1.bt2l
-rw-r--r--  1 a_person a_group   12132 Jan  4 16:01 lambda_virus.2.bt2
-rw-r--r--  1 a_person a_group   24260 Jan  4 16:01 lambda_virus.2.bt2l
-rw-r--r--  1 a_person a_group      17 Jan  4 16:01 lambda_virus.3.bt2
-rw-r--r--  1 a_person a_group      29 Jan  4 16:01 lambda_virus.3.bt2l
-rw-r--r--  1 a_person a_group   12126 Jan  4 16:01 lambda_virus.4.bt2
-rw-r--r--  1 a_person a_group   12126 Jan  4 16:01 lambda_virus.4.bt2l
-rw-r--r--  1 a_person a_group 4210730 Jan  4 16:01 lambda_virus.rev.1.bt2
-rw-r--r--  1 a_person a_group 8405234 Jan  4 16:01 lambda_virus.rev.1.bt2l
-rw-r--r--  1 a_person a_group   12132 Jan  4 16:01 lambda_virus.rev.2.bt2
-rw-r--r--  1 a_person a_group   24260 Jan  4 16:01 lambda_virus.rev.2.bt2l

Modulefiles

The module file is on the system at /usr/local/modulefiles/live/eb/all/Bowtie2/2.3.4.2-foss-2018b.

Alternative installation methods

Bowtie2 is also available via Anaconda. You should be able to install Bowtie 2 with:

conda install bowtie2