Bowtie

Category

Bioinformatics, Aligner

Description

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).

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	1.1.1

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
1.1.1	module load gcc/4.8.2 bowtie/1.1.1

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a bowtie job in batch mode with the following command:

sbatch [Slurm options] --wrap="bowtie [bowtie options]"

Here you need to replace [bowtie options] with bowtie command line options (please run bowtie -h for getting a list of all command line options) and [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of Slurm on the wiki page about the batch system.

License information

Artistic license 1.0

Links

http://bowtie-bio.sourceforge.net/index.shtml

https://en.wikipedia.org/wiki/Bowtie_(sequence_analysis)
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25