Bowtie2¶

Bowtie2 is an ultra fast and memory-efficient tool for aligning sequencing reads to long reference sequences.

Installation¶

You can check the installation documentation here.

Conda¶

conda install -c bioconda bowtie2

Package manager¶

sudo apt update
sudo apt install bowtie2

Manually on Ubuntu/Linux¶

Create and go to install directory

cd $HOME/tools/bowtie2/

Download Ubuntu/Linux version

wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.2/bowtie2-2.4.2-sra-linux-x86_64.zip/download

Decompress

unzip download

Add location to system PATH

export PATH=$HOME/tools/bowtie2/bowtie2-2.4.2-sra-linux-x86_64:$PATH

Check installation¶

bowtie2 --help

Usage¶

$ bowtie2 -h

Usage:   bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> |
         --interleaved <i>} -S [<sam>]

For full usage documentation, run bowtie2 -h.

Example job¶

Serial job¶

Here is an example job running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

# Prepare example genomes in <inputDir>
# Output is stored in <outputDir>
bowtie2-build <inputDir> <outputDir>
bowtie2-inspect <outputDir>

Links¶

Reference¶

Hania Kranas