Maq

Description

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

Documentation:

• Maq User Manual
• Maq Reference Manual
• Maq FAQ

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.