UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing

By Robert C. Edgar. bioRxiv, 2016

1,539 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a9867e89687a6fb581e664c8880e7438af8c8b5a

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Citations in the corpus

Root exudates mediate plant defense against foliar pathogens by recruiting beneficial microbes (2020, methodology): “OTUs were clustered at 100% similarity with UNOISE3, which has a built-in error correction to reduce the influence of sequencing errors (Edgar, 2016).”
Assessing different components of diversity across a river network using eDNA (2019, background): “UNOISE3 has a build‐in error correction to reduce the influence of sequencing er‐ rors (Edgar, 2016).”
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (2017, background): “…have been developed that resolve sequence variants (SVs) from Illumina-scale amplicon data without imposing the arbitrary dissimilarity thresholds that define molecular OTUs (Eren et al, 2013; Tikhonov et al, 2015; Eren et al, 2015; Callahan et al, 2016a; Callahan et al, 2016b; Edgar, 2016).”
Updating the 97% identity threshold for 16S ribosomal RNA OTUs (2017, background): “I have previously called this a ZOTU (zero-radius OTU) (Edgar, 2016); it has also been called a Sequence Variant (Callahan et al., 2016).”
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing (2021, methodology): “OTUs generated by$97% clustering Qiime1, ASVs generated by DADA2 denoising (48), and zOTUs generated by the USEARCH denoising algorithm (49, 99).”
MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples (2020, neutral): “2012; Edgar 2016).”
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing (2021, background): “Furthermore, state-of-the-art clustering algorithms depend on the abundance of unique sequences to model errors 31,32 , which is not suitable for datasets where population micro-heterogeneity is high and evenness low.”
A practical guide to DNA metabarcoding for entomological ecologists (2020, methodology): “Currently, the DADA2 pipeline (Callahan et al., 2016) and UNOISE algorithm (Edgar, 2016) can produce such higher-resolution analogues of the traditional OTUs.”
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns (2017, positive): “Similar in concept to AmpliconNoise (5), a denoising method for pyrosequencing, Deblur, like DADA2 (6) and UNOISE2 (7), attempts to obtain single-nucleotide resolution from Illumina data with statistical methods to infer the putative true sequences within a sample that give rise to the distribution ”