Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

By S. Brown, A. Veach, Anne R. Rigdon-Huss, K. Grond, Spencer K. Lickteig, K. Lothamer, A. Oliver, A. Jumpponen. 2015

221 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/fdb31fdc63534e499af1f11b901374657f1e02e1

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Citations in the corpus

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates (2017, methodology): “The proportion of erroneous singletons has been estimated to 38% on average 12 , and studies of bacterial mock communities have revealed that standard bioinformatic approaches result in many spurious OTUs 13 .”
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, background): “27 Noise generated by this 454 pyrosequencing technology affected different aspects of metagenomic data analysis and led to biased results.”
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015, methodology): “Following exclusion of singletons from all HTS data sets (cf. Brown et al. 2015), representative sequences were selected for each OTU based on the greatest similarity to the consensus sequence.”
Nitrogen addition alters ectomycorrhizal fungal communities and soil enzyme activities in a tropical montane forest (2017, methodology): “OTUs with fewer than 10 sequences (n ¼ 655) were excluded from alpha and beta diversity analyses to provide a robust data set to compare EM fungal communities among N treatments and host developmental stages (Smith and Peay, 2014; Brown et al., 2015).”
Soil fungal communities respond compositionally to recurring frequent prescribed burning in a managed southeastern US forest ecosystem (2015, background): “Low frequency OTUs (representing 6 10 sequences) that may be PCR and/or sequencing artifacts were removed (Tedersoo et al., 2010; Brown et al., 2015) resulting in a total of 1412 OTUs and 348,994 total sequences in the dataset.”
Effect of post-harvest starvation and rinsing on the microbial numbers and the bacterial community composition of mealworm larvae (Tenebrio molitor) (2017, methodology): “Global singletons (i.e. OTUs representing only a single unique sequence in the entire dataset) were removed after UPARSE clustering in order to minimize the risk of retaining sequences from sequencing errors (Brown et al., 2015; Waud, Busschaert, Ruyters, Jacquemyn, & Lievens, 2014).”