MIRA: Difference between revisions

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[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Genomics]][[Category:Assembly]]
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{|<!--CONFIGURATION: REQUIRED-->
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[[Category:Software]][[Category:Bioinformatics]]
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|mira}}
|{{#vardefine:app|mira}}
|{{#vardefine:url|https://sourceforge.net/projects/mira-assembler/}}
|{{#vardefine:url|http://mira-assembler.sourceforge.net/}}
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:exe|}}           <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:job|}}           <!--JOB SCRIPTS-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
|}
<!--BODY-->
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<!--Description-->
<!--Description-->
{{#if: {{#var: url}}|
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}


MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit [http://sourceforge.net/apps/mediawiki/mira-assembler/ the app website] for more details.
 
<!--Modules-->
<!--Modules-->
==Environment Modules==
==Required Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
[[Modules|modules documentation]]
===Serial===
*{{#var:app}}
==System Variables==
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
 
==Documentation==
<!--Configuration-->
The main documentation source for MIRA is the [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html Definitive guide to MIRA].
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
{{#if: {{#var: conf}}|==Configuration==
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
<!--Run-->
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: exe}}|==Additional Information==
 
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
WRITE USAGE POLICY HERE (Licensing, usage, access).
 
|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==
{{#if: {{#var: testing}}|==Performance==
 
WRITE PERFORMANCE TESTING RESULTS HERE|}}
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
If you publish research that uses {{{app}}} you have to cite it as follows:
 
WRITE CITATION HERE
WRITE_CITATION_HERE
 
|}}
|}}
<!--Installation-->
=Validation=
{{#if: {{#var: installation}}|==Installation==
* Validated 4/5/2018
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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__NOTOC____NOEDITSECTION__

Revision as of 18:04, 27 May 2022

Description

mira website  

MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit the app website for more details.

Required Modules

modules documentation

Serial

  • mira

System Variables

  • HPC_MIRA_DIR - installation directory
  • HPC_MIRA_BIN - executable directory
  • HPC_MIRA_DOC - documentation directory

Documentation

The main documentation source for MIRA is the Definitive guide to MIRA.




Validation

  • Validated 4/5/2018
Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=MIRA&oldid=22753"