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bowtie-software
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bowtie-software [2014/10/17 07:50] joguya created |
bowtie-software [2015/07/23 09:58] joguya |
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| * 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). | * 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). | ||
| * For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive. | * For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive. | ||
| - | * There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp. | ||
| - | * [[http:// | ||
| - | ===== Bowtie 1 ===== | + | ===== Information |
| - | ==== v1.1.1 ==== | + | |
| - | === Usage === | + | |
| - | * show all versions of bowtie< | + | |
| - | ---------------------------------------------------------------------------------------------- / | + | * Version: |
| - | bowtie/ | + | * Added: October, 2014 |
| - | </ | + | * Updated: July, 2015 |
| - | * load a specific version, e.g. v1.1.1: < | + | * Link: http://bowtie-bio.sourceforge.net/index.shtml |
| - | * get quick help:< | + | |
| - | === Installation | + | ===== Usage ===== |
| - | * bowtie comes already compiled, so all you have to do is unzip & copy to export-apps< | + | |
| - | unzip bowtie-1.1.1-linux-x86_64.zip | + | |
| - | sudo mkdir / | + | |
| - | sudo cp -r bowtie-1.1.1/ | + | |
| - | </ | + | |
| - | * create module file:< | + | |
| - | ##################################################################### | + | |
| - | ## | + | |
| - | ## bowtie Modulefile | + | |
| - | ## By James Oguya, j.oguya@cgiar.org | + | |
| - | ## October, 2014 | + | |
| - | ## | + | |
| - | set appname | + | === See versions of bowtie |
| - | set version | + | < |
| - | set prefix | + | |
| - | set exec_prefix | + | |
| - | set url " | + | |
| - | set msg " | + | |
| - | module-whatis | + | === Load and run bowtie === |
| + | < | ||
| + | $ bowtie</ | ||
| - | proc ModulesHelp { } { | ||
| - | puts stderr " | ||
| - | } | ||
| - | conflict | + | ===== Installation ====== |
| + | Notes from the sysadmin during installation: | ||
| + | |||
| + | < | ||
| + | unzip bowtie-1.1.2-linux-x86_64.zip | ||
| + | cd bowtie-1.1.2 | ||
| + | sudo mkdir / | ||
| + | sudo cp -r . / | ||
| + | </ | ||
| - | prepend-path | ||
| - | * push the new module using ansible< | ||
bowtie-software.txt · Last modified: 2020/04/27 11:13 by aorth
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