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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
GNU General Public License v3.0
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Genome size normalization #108

Closed ramanujamr closed 1 year ago

ramanujamr commented 1 year ago

Hi Firstly, thank you for developing this excellent tool. I am testing this on some datasets and wanted to know if the final relative abundances are normalized by genome size.

shenwei356 commented 1 year ago

mOTUs are a marker-gene-based profiling tool, which should no need to normalize the abundance by genome size.

AlessioMilanese commented 1 year ago

Thank you for your message and your interest in mOTUs.

mOTUs is based on 10 universal single copy marker genes. These marker genes are present in a single copy in all genomes, regardless of their size. As a result, the final relative abundance is not influenced by the size or complexity of the genomes involved, and can be considered to be normalized by genome size.

you can see an example in Supplementary Figure 1 of the mOTUs2 paper: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-08844-4/MediaObjects/41467_2019_8844_MOESM1_ESM.pdf

ramanujamr commented 1 year ago

Thank you! I appreciate the detailed clarification.