Difference between revisions of "Maq"

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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
* Validated 4/5/2018

Revision as of 15:45, 5 April 2018


maq website  

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


Required Modules

modules documentation


  • maq

System Variables

  • HPC_{{#uppercase: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:

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.


  • Validated 4/5/2018