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fmalmeida / bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
https://bacannot.readthedocs.io/en/latest/
GNU General Public License v3.0
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Add DRAM #22

Closed fmalmeida closed 2 years ago

fmalmeida commented 3 years ago

Check and study the possibility of adding DRAM to the pipeline.

Will it be good? Will it be possible? How to do it?

fmalmeida commented 2 years ago

In the DRAM manual, the following piece of information is given:

Setting up DRAM with KEGG Genes and UniRef90 will take up ~500 GB of storage after processing and require ~512 GB of RAM while using KOfam and skipping UniRef90 will mean all processed databases will take up ~30 GB on disk and will only use ~128 GB of RAM while processing.

Thus, this software is not in compliance with the idea of this pipeline that is to make a generic but comprehensive annotation that is lightweight and has small memory requirements so it easily runs in any machine, from laptops to HPCs.