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The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the process is repeated until convergence. Since it was originally designed to be used on ancient DNA, it supports a position specific substitution matrix, which improves both alignment and consensus calling on chemically damaged aDNA.

MIA has been used to assemble a number of Neandertal and early modern human mitochondria. Occasionally it has been used on smallish nuclear regions, but it will probably not scale to a genome wide analysis.

Required Modules


  • mia

System Variables

  • HPC_{{#uppercase:mia}}_DIR - installation directory
  • HPC_{{#uppercase:mia}}_BIN - executable directory
  • HPC_{{#uppercase:mia}}_MAT - matrix directory


  • Validated 4/5/2018