MIA: Difference between revisions
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m Text replacement - "#uppercase" to "uc" |
No edit summary |
||
| Line 23: | Line 23: | ||
<!--Modules--> | <!--Modules--> | ||
== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
< | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| Line 72: | Line 62: | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
Revision as of 20:48, 10 June 2022
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.
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