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Understanding and mitigating some limitations of Illumina© MiSeq for environmental sequencing of Fungi

https://doi.org/10.1101/184960
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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.1107openalex-snapshot
An Illumina metabarcoding pipeline for fungi
inferredcites →https://doi.org/10.1007/s13225-013-0225-xopenalex-snapshot
Factors shaping community structure of endophytic fungi–evidence from the Pinus-Viscum-system
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/10.1016/j.funeco.2014.08.006openalex-snapshot
Scraping the bottom of the barrel: are rare high throughput sequences artifacts?
inferredcites →https://doi.org/10.1016/j.jid.2016.10.033openalex-snapshot
Performing Skin Microbiome Research: A Method to the Madness
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
inferredcites →https://doi.org/10.1101/125724openalex-snapshot
Index switching causes “spreading-of-signal” among multiplexed samples in Illumina HiSeq 4000 DNA sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12065openalex-snapshot
ITS 1 versus ITS 2 as DNA metabarcodes for fungi
inferredcites →https://doi.org/10.1111/2041-210x.12073openalex-snapshot
Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
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.1462-2920.2010.02193.xopenalex-snapshot
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
inferredcites →https://doi.org/10.1111/mec.12481openalex-snapshot
Towards a unified paradigm for sequence‐based identification of fungi
inferredcites →https://doi.org/10.1111/mec.13719openalex-snapshot
Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field‐based tree experiment
inferredcites →https://doi.org/10.1111/nph.12243openalex-snapshot
Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
inferredcites →https://doi.org/10.1111/nph.12923openalex-snapshot
Parsing ecological signal from noise in next generation amplicon sequencing
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/jcm.43.10.5122-5128.2005openalex-snapshot
Comparison of Six DNA Extraction Methods for Recovery of Fungal DNA as Assessed by Quantitative PCR
inferredcites →https://doi.org/10.1186/2047-217x-1-7openalex-snapshot
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
inferredcites →https://doi.org/10.1186/gb-2010-11-10-r106openalex-snapshot
Differential expression analysis for sequence count data
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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.pcbi.1003553openalex-snapshot
A Toolbox for Representational Similarity Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
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/10.1371/journal.pone.0054583openalex-snapshot
Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.3897/mycokeys.10.4852openalex-snapshot
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
inferredcites →https://doi.org/10.7717/peerj.2823openalex-snapshot
An extensive comparison of species-abundance distribution models

What points at this work

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

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Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana
inferred← citeshttps://doi.org/10.1101/210641openalex-snapshot
Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest
inferred← citeshttps://doi.org/10.1128/aem.00361-23openalex-snapshot
Impact of Wood Age on Termite Microbial Assemblages
inferred← citeshttps://doi.org/10.1128/aem.02042-20openalex-snapshot
Termites Are Associated with External Species-Specific Bacterial Communities
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