Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
The basic idea of this program is to align DNA sequencing fragments(shotgun or targeted resequencing) to a reference, then call aconsensus. Then the consensus is used as new reference and the processis repeated until convergence. Since it was originally designed to beused on ancient DNA, it supports a position specific substitutionmatrix, which improves both alignment and consensus calling onchemically damaged aDNA.
MIA has been used to assemble a number of Neandertal and early modernhuman mitochondria. Occasionally it has been used on smallish nuclearregions, but it will probably not scale to a genome wide analysis.
This program takes the output of MIA and tries to make sure an assembledmitochondrion is free from contamination. It works by looking forpositions in the called consensus where it differs from a panel of knownhuman mitochondria, then classifies each read as either belonging to thesample or a putative contaminant.
If you get MIA from the Git repository, you will need the usual buildenvironment (Gcc, Make, ...) and GNU Autotools (autoconf and automake).Installation should work like this: