Difference between revisions of "MIDAS"
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==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 | ||
| + | * {{uc:{{#var:app}}}}_DB - reference database directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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*'''Q:''' **'''A:'''|}} | *'''Q:''' **'''A:'''|}} | ||
<!--Citation--> | <!--Citation--> | ||
| − | {{#if: {{#var: citation}}|==Citation== | + | {{#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 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
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