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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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References for (not using) metabarcoding quantification #373

Open peterjc opened 3 years ago

peterjc commented 3 years ago

Or our synthetic control data suggests read numbers after PCR are only semi-quantifiable as proxies for abundance in the sample, and for our tree nursery reporting we use only presence/absence. Will want citations for this debate:

Quoting Ahmed et al. (2019) used for our soil_nematodes worked example:

However, no mock community study to date has reported a strong correlation between actual abundance and read frequencies, implying that using read frequency data for computing any abundance-based index of a nematode community may produce inaccurate results. The same is true for this study; read number showed no correlation with actual abundance. In microbial ecology, however, read frequency information continues to be used even though the read frequency issue has been shown to transcend beyond studies involving metazoans such as nematodes to microbes, particularly in mixed species samples (Amend et al. 2010, Edgar 2017).

peterjc commented 2 years ago

Lamb et al. (2018) How quantitative is metabarcoding: A meta-analytical approach https://doi.org/10.1111/mec.14920