bowtie-software
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| bowtie-software [2015/03/24 07:36] – joguya | bowtie-software [2020/04/27 11:13] (current) – aorth | ||
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| ====== Bowtie ====== | ====== Bowtie ====== | ||
| - | * 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 [[bowtie2-software|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. | ||
| ===== Information ===== | ===== Information ===== | ||
| - | * Version: 1.1.1 | + | * Version: 1.2.3 |
| * Added: October, 2014 | * Added: October, 2014 | ||
| + | * Updated: April, 2020 | ||
| * Link: http:// | * Link: http:// | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | === See versions of bowtie which are available | + | See versions of bowtie which are available: |
| < | < | ||
| - | === Load and run bowtie === | + | Load one version into your environment |
| - | < | + | < |
| $ bowtie</ | $ bowtie</ | ||
| Line 22: | Line 24: | ||
| Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
| - | < | + | < |
| - | unzip bowtie-1.1.1-linux-x86_64.zip | + | $ wget 'https:// |
| - | sudo mkdir / | + | $ unzip bowtie-1.2.3-linux-x86_64.zip |
| - | sudo cp -r bowtie-1.1.1/* / | + | $ cd bowtie-1.2.3-linux-x86_64 |
| + | $ sudo mkdir -p / | ||
| + | $ sudo cp -r . / | ||
| + | </ | ||
bowtie-software.1427182562.txt.gz · Last modified: 2015/03/24 07:36 by joguya