Bowtie2
Bowtie2 is used for aligning sequence reads to long reference sequences.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | bowtie2/2.5.4 |
| BGSC | N/A |
Note: You can simply use module load bowtie2 to activate the most recently installed version of this software.
Commands
This is a list of commands from the bowtie2 module that we wanted to highlight. Use this online manual for a full list.
| Command | Description |
|---|---|
| bowtie2 | Input Bowtie2 index, sequence reads, outputs SAM alignments |
| bowtie2-build | Input reference sequences, outputs a Bowtie2 index base |
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load bowtie2/2.5.4 # Load bowtie2
bowtie2 -x <bowtie2_index> -1 <#1 paired files> -2 <#2 paired files> -S <filename for SAM output>
Real Example
Has your research group used Bowtie2 in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of Bowtie2.
Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics. 2018 Jul 18. doi: 10.1093/bioinformatics/bty648.
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.