ABySS: Difference between revisions

Revision as of 17:01, 10 August 2012

Description

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.

Required Modules

modules documentation

Serial

abyss

Parallel (MPI)

intel
openmpi
abyss

@@ Line 31: / Line 31: @@
 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.
 <!--Modules-->
-==Execution Environment and Modules==
+==Required Modules==
-To use abyss with the environment modules system at HPC the following commands are available:
+[[Modules|modules documentation]]
-===Single threaded version===
+===Serial===
-Get module information for abyss:
+* {{#var:app}}
- $module spider abyss
+===Parallel (MPI) ===
-Load the application module:
+*intel
- $module load abyss
+*openmpi
+* {{#var:app}}
-===MPI version===
-Load Intel compiler:
- $module load intel/11.1
-Load MPI implementation:
- $module load openmpi/1.4.3
-Load the application module:
- $module load abyss
-'''Note:' since version 1.3.4 the MPI version can be loaded simply as
- $module load abyss/1.3.4-mpi
-To load the single-threaded version of abyss after the MPI version was loaded purge the modules and load abyss module or simply unload the openmpi module and the abyss module will be reloaded to a single-threaded version automatically.
- module purge
- module load abyss
-or
- module unload openmpi
-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
 {{#if: {{#var: exe}}|==How To Run==
 WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}