Difference between revisions of "Maq"
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Moskalenko (talk | contribs) m (Text replace - "<!--Run-->" to "==System Variables== * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory <!--Run--> ") |
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{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|maq}} | |{{#vardefine:app|maq}} | ||
|{{#vardefine:url|http://maq.sourceforge.net/}} | |{{#vardefine:url|http://maq.sourceforge.net/}} | ||
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|{{#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] | ||
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<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | == | + | ==System Variables== |
| − | *{{#var:app}} | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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* HPC_MAQ_BIN - executable directory | * HPC_MAQ_BIN - executable directory | ||
| − | + | <!--Additional--> | |
| − | + | {{#if: {{#var: exe}}|==Additional Information== | |
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From the Maq website: | From the Maq website: | ||
Latest revision as of 19:47, 12 August 2022
Description
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.