Maq: Difference between revisions
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* [http://maq.sourceforge.net/faq.shtml Maq FAQ] | * [http://maq.sourceforge.net/faq.shtml Maq FAQ] | ||
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== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
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Revision as of 18:31, 10 June 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.