bowtie
Link to section 'Introduction' of 'bowtie' Introduction
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
For more information, please check its website: https://biocontainers.pro/tools/bowtie and its home page: http://bowtie-bio.sourceforge.net/.
Link to section 'Versions' of 'bowtie' Versions
- 1.3.1
Link to section 'Commands' of 'bowtie' Commands
- bowtie
- bowtie-build
- bowtie-inspect
Link to section 'Module' of 'bowtie' Module
You can load the modules by:
module load biocontainers
module load bowtie
Link to section 'Example job' of 'bowtie' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Bowtie on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bowtie
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bowtie
bowtie-build ref.fasta ref
bowtie -p 4 -x ref -1 input_1.fq -2 input_2.fq -S test.sam