Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.
Citations
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1,977 citations
Cites background or methods from "Minimum entropy decomposition: unsu..."
...…been developed that resolve amplicon sequence variants (ASVs) 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; Edgar, 2016; Amir et al., 2017)....
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...ASV methods have demonstrated sensitivity and specificity as good or better than OTU methods and better discriminate ecological patterns (Eren et al., 2013; Eren et al., 2015; Callahan et al., 2016a; Needham et al., 2017)....
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...And the ASV methods that are now available provide better resolution and accuracy than OTU methods (Eren et al., 2015; Callahan et al., 2016a)....
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1,181 citations
Cites methods from "Minimum entropy decomposition: unsu..."
...We omitted classic OTU methods and MED (10), given the benchmarks described in reference 6....
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1,038 citations
Additional excerpts
...…Armbrust, 2010), probabilistic taxonomic placement (e.g., PROTAX (Somervuo, Koskela, Pennanen, Henrik Nilsson, & Ovaskainen, 2016; Somervuo et al., 2017), minimum entropy decomposition (e.g., oligotyping, Eren et al., 2015), MEGAN (Huson, Auch, Qi, & Schuster, 2007) and ecotag (Boyer et al., 2016)....
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1,032 citations
References
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"Minimum entropy decomposition: unsu..." refers methods in this paper
...As recently described, oligotyping (Eren et al., 2013a) also employs a form of signature analysis by using Shannon entropy (Shannon, 1948) to distinguish biologically meaningful signals from noise without requiring the calculation of pairwise sequence similarity....
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28,911 citations
"Minimum entropy decomposition: unsu..." refers methods in this paper
...For OTU clustering, we used QIIME v1....
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..., 2009), QIIME (Caporaso et al., 2010), CD-HIT Suite (Huang et al....
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...Various software platforms, including mothur (Schloss et al., 2009), QIIME (Caporaso et al., 2010), CD-HIT Suite (Huang et al., 2010) and VAMPS (Huse et al., 2014), have adopted most of these OTU identification strategies....
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...5 (Caporaso et al., 2010) with UCLUST (Edgar, 2010) in de novo mode via the pick_otus....
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...5 (Caporaso et al., 2010) with UCLUST (Edgar, 2010) in de novo mode via the pick_otus.py script....
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18,256 citations
"Minimum entropy decomposition: unsu..." refers background in this paper
...…classification of sequences through comparison with curated databases, for example, GreenGenes (DeSantis et al., 2006; McDonald et al., 2012) or SILVA (Pruesse et al., 2007; Quast et al., 2013) and (ii) de novo clustering by sequence similarity to define operational taxonomic units (OTUs)....
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...The two major approaches for partitioning large datasets include: (i) taxonomic classification of sequences through comparison with curated databases, for example, GreenGenes (DeSantis et al., 2006; McDonald et al., 2012) or SILVA (Pruesse et al., 2007; Quast et al., 2013) and (ii) de novo clustering by sequence similarity to define operational taxonomic units (OTUs)....
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..., 2012) or SILVA (Pruesse et al., 2007; Quast et al., 2013) and (ii) de novo clustering by sequence similarity to define operational taxonomic units (OTUs)....
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