Difference between revisions of "Applications/Bowtie1"

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[username@login01 ~]$ module load bowtie1/1.1.21
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[username@login01 ~]$ module add bowtie1/1.1.21
  
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===Batch Job===
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<!-- example from: https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/sequence-alignment-bowtie -->
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<pre>
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#!/bin/bash
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#SBATCH -J bowtie_testing
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#SBATCH -n 4
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#SBATCH -t 1:00:00
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#SBATCH -p=compute
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#SBATCH -o %N.%j.out
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#SBATCH -e %N.%j.err
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module load bowtie1/1.1.21 samtools/gcc/1.3.1
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# Run bowtie
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bowtie dmel5 -p 4 /gpfs/data/shared/biomed/example_fastq/rna_seq/s1_r1.fastq  -S s1_r1.sam
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# Bowtie only give sam format output, if you need bam format, use samtools
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samtools view -bS s1_r1.sam > s1_r1.bam
 
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* [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]
 
* [http://bowtie-bio.sourceforge.net/tutorial.shtml http://bowtie-bio.sourceforge.net/tutorial.shtml]
  
 
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{{Modulepagenav}}
{|
 
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
|style="width:95%; border-width: 0" |
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]]
 
* [[General|General]]
 
* [[Training|Training]]
 
* [[Programming|Programming support]]
 
|-
 
|}
 

Latest revision as of 10:45, 17 November 2022

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:



[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





Modules | Main Page | Further Topics