Difference between revisions of "ABySS"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:Bioinformatics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in temp...")
 
 
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[[Category:Software]][[Category:Bioinformatics]]
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[[Category:Software]][[Category:Biology]][[Category:De Novo]]
<!-- ########  Template Configuration ######## -->
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{|<!--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:app|abyss}}
 
|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
 
|{{#vardefine:url|http://www.bcgsc.ca/platform/bioinfo/software/abyss}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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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.
 
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-->
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<!--Modules-->
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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==Environment Modules==
==Available versions==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* 1.3.1 - single threaded
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==System Variables==
<!-- -->
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
{{#if: {{#var: mod}}|==Running the application using modules==
 
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
 
* HPC_ABYSS_BIN - executable directory
 
* HPC_ABYSS_DOC - documents directory
 
* HPC_ABYSS_MAN - manpages directory
 
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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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:
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export HPC_USE_MPIEXEC=1
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|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 16:17, 19 August 2022

Description

abyss 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.

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