Difference between revisions of "Maq"
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Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
* HPC_MAQ_BIN - executable directory | * HPC_MAQ_BIN - executable directory | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
From the Maq website: | From the Maq website: | ||
Revision as of 17:22, 10 August 2012
Description
Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
Documentation:
Required Modules
Serial
- maq
- HPC_MAQ_BIN - executable directory
System Variables
- HPC_{{#uppercase:maq}}_DIR - installation directory
How To Run
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.