Difference between revisions of "MIDAS"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|midas}} |{{#vardefine:url|https://github.com/snayfach/MI...") |
|||
| Line 10: | Line 10: | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
Revision as of 14:29, 1 September 2016
Description
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.
Required Modules
Serial
- gcc/5.2.0
- midas
System Variables
- HPC_{{#uppercase:midas}}_DIR - installation directory
Citation
If you publish research that uses midas 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.]