ABySS

Description

{{{name}}} website  
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Template:App Location

Available versions

• 1.3.1 - single threaded and MPI ( loading of intel/11.1 and openmpi/1.4.3 modules required)

Running the application using modules

To use abyss with the environment modules system at HPC the following commands are available:

Get module information for abyss:

$module spider abyss

Load Intel compiler:

$module load intel/11.1

Load MPI implementation:

$module load openmpi/1.4.3

Load the default application module:

$module load abyss

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_ABYSS_DIR - directory where abyss is located.
• HPC_ABYSS_BIN - executable directory
• HPC_ABYSS_DOC - documents directory
• HPC_ABYSS_MAN - manpages directory

To load the single-threaded version of abyss purge the modules and load abyss module or simply unload the openmpi module and the abyss module will be switched to a single-threaded version automatically.

module purge
module load abyss