bowtie2-software
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| bowtie2-software [2017/12/25 21:35] – aorth | bowtie2-software [2022/11/21 08:16] (current) – aorth | ||
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| ====== Bowtie 2====== | ====== Bowtie 2====== | ||
| - | * 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. |
| + | |||
| + | There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp. | ||
| + | |||
| + | [[https:// | ||
| ===== Information ===== | ===== Information ===== | ||
| - | * Version: 2.3.3 | + | * Version: 2.5.0 |
| * Added: March, 2015 | * Added: March, 2015 | ||
| - | * Updated: | + | * Updated: |
| - | * Link: http:// | + | * Link: https:// |
| ===== Usage ===== | ===== Usage ===== | ||
| - | See versions | + | See versions which are available: |
| < | < | ||
| - | Load and run bowtie2: | + | Load one version into your environment |
| - | < | + | < |
| $ bowtie2</ | $ bowtie2</ | ||
| Line 26: | Line 30: | ||
| < | < | ||
| - | $ wget 'https://downloads.sourceforge.net/ | + | $ wget https://liquidtelecom.dl.sourceforge.net/ |
| - | $ unzip bowtie2-2.3.3-linux-x86_64.zip | + | $ unzip bowtie2-2.5.0-linux-x86_64.zip |
| - | $ sudo mkdir / | + | $ sudo cp -r bowtie2-2.5.0-linux-x86_64/* / |
| - | sudo cp -rv bowtie2-2.3.3/* / | + | |
bowtie2-software.1514237756.txt.gz · Last modified: 2017/12/25 21:35 by aorth