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--- bowtie2-software [2017/09/20 09:04] – aorth
+++ bowtie2-software [2025/03/03 07:29] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== 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).
-  * 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.
+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).
-  * There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
-  * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1| differences between Bowtie1 & Bowtie2]]
+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://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1| Differences between Bowtie1 and Bowtie2]].
 ===== Information =====
-  * Version: 2.3.3
+  * Version: 2.5.4
   * Added: March, 2015
-  * Updated: September, 2017
+  * Updated: March, 2025
-  * Link: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+  * Link: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
 ===== Usage =====
-=== See versions of bowtie2 which are available ===
+See versions which are available:
 <code>$ module avail bowtie2</code>
-=== Load and run bowtie2 ===
+Load one version into your environment and run it:
-<code>$ module load bowtie2/2.3.3
+<code>$ module load bowtie2/2.5.4
 $ bowtie2</code>
@@ Line 26: / Line 30: @@
 <code>$ cd /tmp
-$ wget 'https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.3/bowtie2-2.3.3-linux-x86_64.zip?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.3.3&ts=1505896186&use_mirror=netix' -O bowtie2-2.3.3-linux-x86_64.zip
+$ wget https://github.com/BenLangmead/bowtie2/releases/download/v2.5.4/bowtie2-2.5.4-linux-x86_64.zip
-$ unzip bowtie2-2.3.3-linux-x86_64.zip
+$ unzip bowtie2-2.5.4-linux-x86_64.zip
-$ sudo mkdir /export/apps/bowtie2/2.3.3
+$ sudo cp -r bowtie2-2.5.4-linux-x86_64 /export/apps/bowtie2/2.5.4</code>
-sudo cp -rv bowtie2-2.3.3/* /export/apps/bowtie2/2.3.3</code>