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Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

https://doi.org/10.1101/213470
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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/b978-0-12-372180-8.50042-1openalex-snapshot
AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS
inferredcites →https://doi.org/10.1016/j.funeco.2015.03.003openalex-snapshot
Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %
inferredcites →https://doi.org/10.1038/ismej.2011.74openalex-snapshot
Illumina-based analysis of microbial community diversity
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btp450openalex-snapshot
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
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/bioinformatics/btw753openalex-snapshot
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
inferredcites →https://doi.org/10.1093/molbev/msn188openalex-snapshot
Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought
inferredcites →https://doi.org/10.1093/nar/gkr771openalex-snapshot
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
inferredcites →https://doi.org/10.1093/nar/gkv107openalex-snapshot
Accurate multiplexing and filtering for high-throughput amplicon-sequencing
inferredcites →https://doi.org/10.1093/nar/gkw984openalex-snapshot
Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing
inferredcites →https://doi.org/10.1101/gr.5457707openalex-snapshot
Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
inferredcites →https://doi.org/10.1111/1755-0998.12951openalex-snapshot
An improved method for utilizing high‐throughput amplicon sequencing to determine the diets of insectivorous animals
inferredcites →https://doi.org/10.1111/j.1365-294x.1993.tb00005.xopenalex-snapshot
ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03160.xopenalex-snapshot
The UNITE database for molecular identification of fungi – recent updates and future perspectives
inferredcites →https://doi.org/10.1111/nph.12923openalex-snapshot
Parsing ecological signal from noise in next generation amplicon sequencing
inferredcites →https://doi.org/10.1111/nph.14776openalex-snapshot
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
inferredcites →https://doi.org/10.1128/aem.00905-17openalex-snapshot
Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity
inferredcites →https://doi.org/10.1128/aem.02576-16openalex-snapshot
Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing
inferredcites →https://doi.org/10.1128/aem.02639-15openalex-snapshot
Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules
inferredcites →https://doi.org/10.1186/1471-2164-12-382openalex-snapshot
Addressing challenges in the production and analysis of illumina sequencing data
inferredcites →https://doi.org/10.1186/gb-2011-12-2-r18openalex-snapshot
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
inferredcites →https://doi.org/10.1186/s40168-017-0267-5openalex-snapshot
Optimizing methods and dodging pitfalls in microbiome research
inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
inferredcites →https://doi.org/10.1371/journal.pone.0043093openalex-snapshot
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s11104-023-05896-wopenalex-snapshot
Legacy effects post removal of a range-expanding shrub influence soil fungal communities and create negative plant-soil feedbacks for conspecific seedlings
inferred← citeshttps://doi.org/10.1093/gigascience/giz092openalex-snapshot
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
inferred← citeshttps://doi.org/10.1093/jmammal/gyy044openalex-snapshot
Incidence and taxonomic richness of mosquitoes in the diets of little brown and big brown bats
inferred← citeshttps://doi.org/10.1111/1755-0998.13294openalex-snapshot
MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction
inferred← citeshttps://doi.org/10.3390/life8020019openalex-snapshot
Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities
inferred← citeshttps://doi.org/10.70675/566f36f5z4361z4a72z83f4z6abd401a4af9openalex-snapshot
Étude du rôle fonctionnel du microbiote intestinal dans l'adaptation à un régime sous optimal et dans l'efficience alimentaire de la poule pondeuse en utilisant une approche multi-omique.
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