Difference between revisions of "MIA"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|mia}} |{{#vardefine:url|https://github.com/udo-stenzel/mapp...") |
|||
| (3 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|mia}} | |{{#vardefine:app|mia}} | ||
| 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_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_MAT - matrix directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 19:52, 12 August 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