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maq website  

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


Environment Modules

Run module spider maq to find out what environment modules are available for this application.

System Variables

  • HPC_MAQ_DIR - installation directory
  • HPC_MAQ_BIN - executable directory

Additional Information

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: 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;
maqview -c consensus.cns

Even for advanced maq users, running ` demo' is recommended. You may find something helpful.