Difference between revisions of "Applications/Bowtie1"
From HPC
(Created page with "==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 ove...") |
m |
||
Line 1: | Line 1: | ||
+ | __TOC__ | ||
+ | |||
==Application Details== | ==Application Details== | ||
Line 37: | Line 39: | ||
* [[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 load bowtie1/1.1.21 |
</pre> | </pre> |
Revision as of 08:16, 6 April 2017
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: bowtie1/1.1.2
- 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 load bowtie1/1.1.21
Further Information