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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 controls #319

Open peterjc opened 3 years ago

peterjc commented 3 years ago

Meta-issue for things we should probably cite in our write-up

Sepulveda et al. (2020) The Elephant in the Lab (and Field): Contamination in Aquatic Environmental DNA Studies https://doi.org/10.3389/fevo.2020.609973

Has a nice tables of studies and their controls, lots took the "Set as background level" route we use with negative controls raising our minimum abundance threshold.

See also #318

peterjc commented 3 years ago

The context is different (metagenomes rather than markers), but another example with shuffled sequences as negative controls:

Lindgreen et al. (2016) An evaluation of the accuracy and speed of metagenome analysis tools https://doi.org/10.1038/srep19233

peterjc commented 3 years ago

Also this fungal paper, they made 12 synthetic ITS1 like sequences for use in a mock community:

Palmer et al. (2018) Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data https://doi.org/10.7717/peerj.4925

They made some similar conclusions:

While the data presented here do not support using read abundance as a proxy for biological abundance in HTAS studies, it does support use of presence/absence (binary) metrics ...