bowtie2-software
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Table of Contents
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.
- There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
Information
- Version: 2.3.3
- Added: March, 2015
- Updated: September, 2017
Usage
See versions of bowtie2 which are available
$ module avail bowtie2
Load and run bowtie2
$ module load bowtie2/2.3.3 $ bowtie2
Installation
Notes from the sysadmin during installation:
$ 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 $ unzip bowtie2-2.3.3-linux-x86_64.zip $ sudo mkdir /export/apps/bowtie2/2.3.3 sudo cp -rv bowtie2-2.3.3/* /export/apps/bowtie2/2.3.3
bowtie2-software.1505898273.txt.gz · Last modified: 2017/09/20 09:04 by aorth