Applications/Bowtie1

Application Details

• 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).
• Version: 1.1.2
• Modules: bowtie/1.1.2
• Licence: Open source (Github)

Usage Examples

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

It provides the following tools:

• bowtie
• bowtie-align-l
• bowtie-align-l-debug
• bowtie-align-s
• bowtie-align-s-debug
• bowtie-build
• bowtie-buildc
• bowtie-build-l
• bowtie-build-l-debug
• bowtie-build-s
• bowtie-build-s-debug
• bowtie-inspect
• bowtie-inspect-l
• bowtie-inspect-l-debug
• bowtie-inspect-s
• bowtie-inspect-s-debug

With linkages to the following modules too:

• Cufflinks
• Samtools
• Tophat
• Samtools
• Bowtie2

[username@login01 ~]$ module add bowtie1/1.1.21

Batch Job

#!/bin/bash

#SBATCH -J bowtie_testing
#SBATCH -n 4
#SBATCH -t 1:00:00
#SBATCH -p=compute
#SBATCH -o %N.%j.out
#SBATCH -e %N.%j.err

module load bowtie1/1.1.21 samtools/gcc/1.3.1

# Run bowtie
bowtie dmel5 -p 4 /gpfs/data/shared/biomed/example_fastq/rna_seq/s1_r1.fastq   -S s1_r1.sam

# Bowtie only give sam format output, if you need bam format, use samtools
samtools view -bS s1_r1.sam > s1_r1.bam

Further Information

• http://bowtie-bio.sourceforge.net/tutorial.shtml

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