Bowtie2 is a fast, multi-threaded, and memory efficient aligner for short read sequences. Bowtie uses a Burrows-Wheeler index to achieve a moderate memory footprint of 2 - 4 GB depending on genome size and alignment parameters. Performance generally scales well with thread count.
Documentation
Bowtie2 Home Page
Bowtie2 Manual
Slurm script
#!/bin/bash #SBATCH --job-name=bowtie2 #SBATCH --time=1:00:00 #SBATCH --partition=norm #SBATCH --ntasks=1 #SBATCH --mem=64GB module load bowtie2 ???
Build instructions for those who are curious
$ git clone --recursive https://github.com/BenLangmead/bowtie2.git
$ cd bowtie2
$ cmake . -D USE_SRA=1 -D USE_SAIS_OPENMP=1 -DCMAKE_INSTALL_PREFIX=/mnt/nasapps/production/bowtie2/2.5.4 && cmake --build .
$ make install