MIA¶
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.
Environment Modules¶
Run module spider MIA to find out what environment modules are available for this application.
System Variables¶
- HPC_MIA_DIR - installation directory
- HPC_MIA_BIN - executable directory
- HPC_MIA_MAT - matrix directory