View source for MIA

[[Category:Software]][[Category:Biology]][[Category:NGS]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|mia}}
|{{#vardefine:url|https://github.com/udo-stenzel/mapping-iterative-assembler}}
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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.

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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_MAT - matrix directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
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{{#if: {{#var: testing}}|==Performance==
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{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE_CITATION_HERE
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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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