Difference between revisions of "Maq"

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[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
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[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|maq}}
 
|{{#vardefine:app|maq}}
 
|{{#vardefine:url|http://maq.sourceforge.net/}}
 
|{{#vardefine:url|http://maq.sourceforge.net/}}
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
 
<!--CONFIGURATION: OPTIONAL (1=ON)-->
|{{#vardefine:mod|1}} <!--MODULES - NOW REQUIRED-->
 
|{{#vardefine:intel|}} <!-- "11.1" - Compiler Module Choice -->
 
|{{#vardefine:mpi|}} <!-- "openmpi/1.3.4"- MPI Module Choice -->
 
 
|{{#vardefine:exe|1}} <!--RUNNING -->
 
|{{#vardefine:exe|1}} <!--RUNNING -->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
 
|{{#vardefine:conf|}} <!--CONFIGS-->
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* [http://maq.sourceforge.net/maq-manpage.shtml Maq Reference Manual]
 
* [http://maq.sourceforge.net/maq-manpage.shtml Maq Reference Manual]
 
* [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 
* [http://maq.sourceforge.net/faq.shtml Maq FAQ]
 
 
 
<!--Modules-->
 
<!--Modules-->
{{#if: {{#var: mod}}|==Execution Environment and Modules==
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==Environment Modules==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below-->
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_MAQ_BIN - executable directory
 
* HPC_MAQ_BIN - executable directory
<!--Run-->
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<!--Additional-->
{{#if: {{#var: exe}}|==How To Run==
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{{#if: {{#var: exe}}|==Additional Information==
 
From the Maq website:
 
From the Maq website:
  
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
<!--Policy-->
 
<!--Policy-->
{{#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)
 
|}}
 
|}}

Latest revision as of 19:47, 12 August 2022

Description

maq website  

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.

Documentation:

Environment Modules

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

System Variables

  • HPC_MAQ_DIR - installation directory
  • HPC_MAQ_BIN - executable directory

Additional Information

From the Maq website:

Follow these steps to run Maq. All you need is a reference sequence file in the FASTA format.

Prepare a reference sequence (ref.fasta), better a bacterial genome to make the test run faster.

Simulate diploid reference and read sequences, map reads, call variants and evaluate the results in one go:

maq.pl demo ref.fasta calib-30.dat

where calib-30.dat is contained in maq-data.

View the alignment:

cd maqdemo/easyrun;
maqindex -i -c consensus.cns all.map;
maqview -c consensus.cns all.map

Even for advanced maq users, running `maq.pl demo' is recommended. You may find something helpful.