Bowtie

Software Summary

Mesabi

Default Module:

2.3.4.1

Other Modules Available:

1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4

Last Updated On:

Monday, October 23, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

2.3.4.1

Other Modules Available:

1.1.2, 2.1.0, 2.2.2, 2.2.4, 2.3.0, 2.3.1, 2.3.2, 2.3.4.1, 2.4.4

Last Updated On:

Monday, October 23, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Monday, October 23, 2023

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Genetics

Software 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).

Software Documentation

Software Documentation Tabs

General Linux

To run this software interactively in a Linux environment run the commands:

module load bowtie
bowtie ...

For bowtie versions 2.0 and above, use the program "bowtie2" instead of simply "bowtie".

To see a list of available options, type the command

bowtie2 -h

Pre-built bowtie indexes for popular genomes are available at

/project/db/genomes/[species]/[build]/bowtie2

Bowtie programs may also be submitted to a queue using PBS script such as the one below:

#PBS -l nodes=3:ppn=8,pmem=1000mb,walltime=8:00:00
#PBS -m abe
#PBS -M sample_email@umn.edu

module load bowtie

bowtie2 -p $PBS_NP reads/e_coli_10000snp.fq ec_snp.sam

Note the use of -p $PBS_NP; this option is used to specify the number of threads used by Bowtie. Also note that only 0.X versions of Bowtie are available on Itasca and Cascade.

Compatibility issues:
Bowtie genome indexes built using 0.X versions are not compatible with indexes built using 2.X versions. Significant changes (improvements) have been made to Bowtie command-line options, and to how Bowtie performs alignments. To see a list of installed Bowtie versions type the command

module show bowtie

Bowtie 0.X genome indexes are available at

/project/db/genomes/[SPECIES]/[BUILD]/bowtie

Additional Information

User Manual