MIA

Description

mia website

The basic idea of Mapping Iterative Assembler (MIA) 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.

Environment Modules

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

Environment Variables

• HPC_MIA_DIR - installation directory
• HPC_MIA_BIN - executable directory
• HPC_MIA_MAT - matrix directory

Categories

biology, ngs