Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by The project page is available at Maq is previously known as mapass2.

Run Maq Now

Follow these steps to try Maq. All you need is a reference sequence file in the FASTA format.

  1. Prepare a reference sequence (ref.fasta). Better a bacterial genome.
  2. Download maq, maq-data and maqview at the download page.
  3. Copy maq, and to the $PATH or to the same directory.
  4. 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.
  5. 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.


Maq is documented in three parts: Maq User's Manual, Maq Reference Manual and FAQ page. The user's manual introduces basic functions in maq, the reference manual gives detailed usage of each function and wiki site presents informal but useful tips and notes related to maq. These documentations are complementary to each other.