MIA
Revision as of 21:21, 6 December 2019 by Moskalenko (talk | contribs) (Text replacement - "#uppercase" to "uc")
Description
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
Serial
- mia
System Variables
- HPC_MIA_DIR - installation directory
- HPC_MIA_BIN - executable directory
- HPC_MIA_MAT - matrix directory
Validation
- Validated 4/5/2018