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...") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (2 intermediate revisions by one other user not shown) | |||
| 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--> | ||
|} | |} | ||
| Line 38: | Line 38: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 72: | Line 72: | ||
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. | |
|}} | |}} | ||
Revision as of 21:21, 6 December 2019
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_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.