Difference between revisions of "Maq"
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Revision as of 02:36, 10 August 2012
Description
Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
Documentation:
Execution Environment and Modules
To use maq with the environment modules system at HPC the following commands are available:
Get module information for maq:
$module spider maq
Load the default application module:
$module load maq
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_MAQ_DIR - directory where maq is located.
- 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.