Difference between revisions of "Maq"

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Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
 
Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
  

Revision as of 01:53, 10 August 2012

Description

maq website  

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.

Documentation:

Template:App Location

Available versions

  • 0.7.1

Running the application using 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.