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Maq

Description

maq website

Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data.

Environment Modules

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

Environment Variables

  • HPC_MAQ_DIR - installation directory
  • HPC_MAQ_BIN - executable directory
  • HPC_MAQ_SAMPLE - directory with a sample data file calib-36.dat

Additional Usage 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.

Categories

biology, ngs