Difference between revisions of "Applications/Bowtie1"
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==Application Details== | ==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). | * 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 | * Version: 1.1.2 | ||
| − | * Modules: | + | * Modules: bowtie/1.1.2 |
* Licence: Open source (Github) | * Licence: Open source (Github) | ||
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* [[applications/Tophat|Tophat]] | * [[applications/Tophat|Tophat]] | ||
* [[applications/Samtools|Samtools]] | * [[applications/Samtools|Samtools]] | ||
| − | * [[ | + | * [[applications/Bowtie2|Bowtie2]] |
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module load | + | [username@login01 ~]$ module add bowtie1/1.1.21 |
| + | |||
| + | </pre> | ||
| + | |||
| + | ===Batch Job=== | ||
| + | <!-- example from: https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/sequence-alignment-bowtie --> | ||
| + | <pre> | ||
| + | #!/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 | ||
</pre> | </pre> | ||
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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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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