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Maq: Mapping and Assembly with Quality

http://maq.sourceforge.net

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/. 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, maq.pl and maq_eval.pl 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:
    maq.pl 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 all.map;
    maqview -c consensus.cns all.map

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