Maq
Revision as of 16:55, 10 August 2012 by Moskalenko (talk | contribs) (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}}")
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
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.