Difference between revisions of "ABySS"

Latest revision as of 16:17, 19 August 2022

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.

Environment Modules

Run module spider abyss to find out what environment modules are available for this application.

System Variables

HPC_ABYSS_DIR - installation directory

How To Run

The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:

export HPC_USE_MPIEXEC=1

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+[[Category:Software]][[Category:Biology]][[Category:De Novo]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|abyss}}
 |{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
 <!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 27: / Line 17: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 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.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Available versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 1.3.1 - single threaded and MPI ( loading of intel/11.1 and openmpi/1.4.3 modules required)
+==System Variables==
-* 1.3.4 - single threaded and MPI versions are provided. Load the abyss/1.4.3-mpi module for the latter version. All dependencies will autoload.
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-<!-- -->
+{{#if: {{#var: exe}}|==How To Run==
-==Running the application using modules==
+The abyss-pe is hardcoded to use mpiexec, so you need to set the following variable in your abyss job script before calling abyss-pe to explicitly allow mpiexec usage, which is disabled by default:
-To use abyss with the environment modules system at HPC the following commands are available:
-'''(Note the warnings you get if you don't load the 'bowtie' and 'bwa' modules)'''
-===Single threaded version===
+  export HPC_USE_MPIEXEC=1
+|}}
-Get module information for abyss:
-  $module spider abyss
-Load the application module:
- $module load abyss
-===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|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==