Fork me on GitHub

bwa

BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx command.

The latest version of bwa (currently 0.7.12) is made available with the command

module load apps/gcc/5.2/bwa

Alternatively, you can load a specific version with

module load apps/gcc/5.2/bwa/0.7.12
module load apps/gcc/5.2/bwa/0.7.5a

This command makes the bwa binary available to your session.

Documentation

Once you have made bwa available to the system using the module command above, you can read the man pages by typing

man bwa

Installation notes

bwa 0.7.12

bwa 0.7.12 was installed using gcc 5.2

module load compilers/gcc/5.2

#build
module load compilers/gcc/5.2
tar -xvjf ./bwa-0.7.12.tar.bz2
cd bwa-0.7.12
make

#Sort out manfile
mkdir -p share/man/man1
mv bwa.1 ./share/man/man1/

#Install
mkdir -p /usr/local/packages6/apps/gcc/5.2/bwa/
cd ..
mv bwa-0.7.12 /usr/local/packages6/apps/gcc/5.2/bwa/0.7.12/

bwa 0.7.5a

bwa 0.7.5a was installed using gcc 5.2

module load compilers/gcc/5.2

#build
module load compilers/gcc/5.2
tar -xvjf bwa-0.7.5a.tar.bz2
cd bwa-0.7.5a
make

#Sort out manfile
mkdir -p share/man/man1
mv bwa.1 ./share/man/man1/

#Install
mkdir -p /usr/local/packages6/apps/gcc/5.2/bwa/
cd ..
mv bwa-0.7.5a /usr/local/packages6/apps/gcc/5.2/bwa/

Testing

No test suite was found.

Module files

The default version is controlled by the .version file at /usr/local/modulefiles/apps/gcc/5.2/bwa/.version

#%Module1.0#####################################################################
##
## version file for bwa
##
set ModulesVersion  "0.7.12"

Version 0.7.12

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/bwa/0.7.12
  • On github: 0.7.12.

Version 0.7.5a

  • The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/bwa/0.7.5a
  • On github: 0.7.5a.