Difference between revisions of "MIDAS"

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(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|midas}} |{{#vardefine:url|https://github.com/snayfach/MI...")
 
 
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* gcc/5.2.0
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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* {{uc:{{#var:app}}}}_DB - reference database directory
 
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<!--Configuration-->
 
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{{#if: {{#var: conf}}|==Configuration==
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*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
<!--Citation-->
 
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
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{{#if: {{#var: citation}}1|==Citation==
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
  
[Nayfach, S. and Pollard, KS. "Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria". bioRxiv 2015.]
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S Nayfach, B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria". Genome Research 2016. doi:10.1101/gr.201863.115
  
 
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Latest revision as of 17:23, 10 June 2022

Description

midas website  

Metagenomic Intra-Species Diversity Analysis System (MIDAS)

MIDAS is an integrated pipeline that leverages >30,000 reference genomes to estimate bacterial species abundance and strain-level genomic variation, including gene content and SNPs, from shotgun metagnomes.

Environment Modules

Run module spider midas to find out what environment modules are available for this application.

System Variables

  • HPC_MIDAS_DIR - installation directory
  • HPC_MIDAS_BIN - executable directory
  • MIDAS_DB - reference database directory




Citation

If you publish research that uses midas you have to cite it as follows:

S Nayfach, B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria". Genome Research 2016. doi:10.1101/gr.201863.115