ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time.
Citations
1,868 citations
Cites methods from "ESPRIT-Tree: hierarchical clusterin..."
...De novo OTU-picking usually relies on unsupervised machine learning methods (Cai and Sun, 2011; Edgar, 2010; Fu et al., 2012) that *To whom correspondence should be addressed....
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...De novo OTU-picking usually relies on unsupervised machine learning methods (Cai and Sun, 2011; Edgar, 2010; Fu et al., 2012) that*To whom correspondence should be addressed....
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527 citations
Cites background from "ESPRIT-Tree: hierarchical clusterin..."
...Particularly, Illumina data, with dozens of samples routinely sequenced at depths over 100 000 reads, are hard to process in a reasonable time (Cai and Sun, 2011; Fu et al., 2012)....
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472 citations
Cites background from "ESPRIT-Tree: hierarchical clusterin..."
...…(Matias Rodrigues and von Mering, 2014)) as well as greedy but more computationally efficient heuristics that perform sequence comparison and OTU identification simultaneously (i.e., ESPRIT-Tree (Cai and Sun, 2011), CD-HIT (Li et al., 2001), UCLUST (Edgar, 2010), DySC (Zheng et al., 2012))....
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...E-mail: meren@mbl.edu Received 13 June 2014; revised 2 September 2014; accepted 7 September 2014; published online 17 October 2014 The ISME Journal (2015) 9, 968–979 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej HPC-CLUST (Matias Rodrigues and von Mering, 2014)) as well as greedy but more computationally efficient heuristics that perform sequence comparison and OTU identification simultaneously (i.e., ESPRIT-Tree (Cai and Sun, 2011), CD-HIT (Li et al., 2001), UCLUST (Edgar, 2010), DySC (Zheng et al., 2012))....
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470 citations
Cites methods from "ESPRIT-Tree: hierarchical clusterin..."
...Therefore, we used three different clustering methods for OTU generation: UCLUST [25], ESPRIT-tree [26] and CD_HIT_OTU [27] (Table S1), which have been proven to generate satisfactory and comparable numbers of OTUs [24]....
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443 citations
References
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"ESPRIT-Tree: hierarchical clusterin..." refers background in this paper
...In addition to microbial diversity estimation, there is currently increased interest in applying taxonomyindependent analysis to analyze millions of sequences for comparative microbial community analysis (11,12)....
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...05 level 241 (7) 268 (6) 362 (11) 314 (9) peak NMI-species 402 (9) 400 (9) 590 (13) 314 (9) peak NMI-genus 190 (5) 176 (7) 216 (6) 243 (7)...
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21,651 citations
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