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Alpha diversity metrics for noisy OTUs

https://doi.org/10.1101/434977
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.funeco.2012.06.003openalex-snapshot
Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?
inferredcites →https://doi.org/10.1038/ismej.2013.141openalex-snapshot
Resistance and resilience of the forest soil microbiome to logging-associated compaction
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nrg3182openalex-snapshot
The human microbiome: at the interface of health and disease
inferredcites →https://doi.org/10.1093/bioinformatics/btr087openalex-snapshot
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
inferredcites →https://doi.org/10.1093/bioinformatics/btv401openalex-snapshot
Error filtering, pair assembly and error correction for next-generation sequencing reads
inferredcites →https://doi.org/10.1093/nar/gkr771openalex-snapshot
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
inferredcites →https://doi.org/10.1101/074252openalex-snapshot
UCHIME2: improved chimera prediction for amplicon sequencing
inferredcites →https://doi.org/10.1101/081257openalex-snapshot
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
inferredcites →https://doi.org/10.1101/124149openalex-snapshot
UNBIAS: An attempt to correct abundance bias in 16S sequencing, with limited success
inferredcites →https://doi.org/10.1101/389833openalex-snapshot
Octave plots for visualizing diversity of microbial OTUs
inferredcites →https://doi.org/10.1101/400762openalex-snapshot
UNCROSS2: identification of cross-talk in 16S rRNA OTU tables
inferredcites →https://doi.org/10.1111/biom.12200openalex-snapshot
An improved nonparametric lower bound of species richness via a modified good–turing frequency formula
inferredcites →https://doi.org/10.1111/j.1462-2920.2010.02193.xopenalex-snapshot
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
inferredcites →https://doi.org/10.1126/science.aac8455openalex-snapshot
The global ocean microbiome
inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
inferredcites →https://doi.org/10.1146/annurev-pathol-011811-132421openalex-snapshot
Human Microbiome in Health and Disease
inferredcites →https://doi.org/10.1186/s13027-016-0112-7openalex-snapshot
Characterisation of microbial communities within aggressive prostate cancer tissues
inferredcites →https://doi.org/10.1186/s13027-017-0168-zopenalex-snapshot
A systematic review on multiparametric MR imaging in prostate cancer detection
inferredcites →https://doi.org/10.1186/s13059-014-0531-yopenalex-snapshot
Temporal variability is a personalized feature of the human microbiome
inferredcites →https://doi.org/10.1371/journal.pone.0094249openalex-snapshot
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys
inferredcites →https://doi.org/10.48550/arxiv.1604.02598openalex-snapshot
Species richness estimation with high diversity but spurious singletons
inferredcites →https://doi.org/10.7717/peerj.3889openalex-snapshot
Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s00027-021-00828-1openalex-snapshot
The network structure of intertidal meiofaunal communities from environmental DNA metabarcoding surveys in Northwest Iberia
inferred← citeshttps://doi.org/10.1016/j.ecss.2020.106683openalex-snapshot
Small-scale spatial variation of meiofaunal communities in Lima estuary (NW Portugal) assessed through metabarcoding
inferred← citeshttps://doi.org/10.1111/jcpe.14067openalex-snapshot
Association Between Dietary Patterns and Subgingival Microbiota: Results From the Oral Infections, Glucose Intolerance, and Insulin Resistance Study ( ORIGINS )
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