Installing Bowtie2

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It works particularly well for reads of about 50 up to hundreds of bases aligned to relatively long genomes (e.g., mammalian). In my opinion, Bowtie2 is one of the most important software tools in genomics (cited ~50K times). Read more about Bowtie2 here: https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

Bowtie2 on Ubuntu/Linux

There are multiple ways to install Bowtie2. Two common methods are described below:

a) Install using conda

conda install -c bioconda bowtie2

b) Install using the package manager (recommended)

sudo apt update
sudo apt install bowtie2

c) Verify the installation

bowtie2 --help

If successful, this will display Bowtie2 help information and version number.

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Bowtie2 on macOS

A. Check if Homebrew is installed

Run:

brew --help

If you get command not found, you need to install Homebrew first. Refer to the Installing FastQC on macOS section for instructions on installing Homebrew.

B. Install Bowtie2 using Homebrew

brew install bowtie2

C. Verify the installation

bowtie2

If successful, this will display Bowtie2 usage information and version number.