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Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive sesssion with the qsh or qrsh command.

The latest version of bowtie2 (currently 2.2.26) is made available with the command

module load apps/gcc/5.2/bowtie2

Alternatively, you can load a specific version with

module load apps/gcc/5.2/bowtie2/2.2.6

This command makes the bowtie2 executables available to your session by adding the install directory to your PATH variable. This allows you to simply do something like the following

bowtie2 --version

which gives results that looks something like

/usr/local/packages6/apps/gcc/5.2/bowtie2/2.2.6/bowtie2-align-s version 2.2.6
64-bit
Built on node063
Fri Oct 23 08:40:38 BST 2015
Compiler: gcc version 5.2.0 (GCC)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Installation notes

bowtie2 2.2.6 was installed using gcc 5.2

#Build
module load compilers/gcc/5.2
unzip bowtie2-2.2.6-source.zip
cd bowtie2-2.2.6
make

#Install
cd ..
mkdir -p /usr/local/packages6/apps/gcc/5.2/bowtie2
mv ./bowtie2-2.2.6 /usr/local/packages6/apps/gcc/5.2/bowtie2/2.2.6

Testing

No test suite was found.

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/bowtie2/2.2.6

The contents of the module file is

#%Module1.0#####################################################################
##
## bowtie2 2.2.6 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

module load compilers/gcc/5.2


proc ModulesHelp { } {
        puts stderr "Makes bowtie 2.2.6 available"
}

set version 2.2.6
set BOWTIE2_DIR /usr/local/packages6/apps/gcc/5.2/bowtie2/$version

module-whatis   "Makes bowtie2 v2.2.6 available"

prepend-path PATH $BOWTIE2_DIR