An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
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...Internal nodes were assigned taxonomic labels using tax2tree (McDonald et al. 2012)....
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Cites methods from "An improved Greengenes taxonomy wit..."
...Challenges in this process include the short length of typical sequencing reads with current technology, sequencing and PCR errors [4], selection of appropriate marker genes that contain sufficient heterogeneity to differentiate target species but that are homogeneous enough in some regions to design broad-spectrum primers, quality of reference sequence annotations [5], and selection of a method that accurately predicts the taxonomic affiliation of millions of sequences at low computational cost....
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...Classification of bacterial/archaeal 16S rRNA gene sequences was made using the Greengenes (13_8 release) [5] reference sequence database preclustered at 99% ID, with amplicons for the domain of interest extracted using primers 27F/1492R [27], 515F/806R [28], or 27F/534R [29] with q2-feature-classifier’s extract_reads method....
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...the classic precision, recall, and F-measure metrics [5] (novel taxa use the standard calculations as described below, but modified definitions for true positive (TP), false positive (FP), and false negative (FN), as described...
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References
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"An improved Greengenes taxonomy wit..." refers methods in this paper
...In this paper, we found that retraining the RDP classifier (Wang et al., 2007) using taxa from the An improved Greengenes taxonomy D McDonald et al...
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...In this paper, we found that retraining the RDP classifier (Wang et al., 2007) using taxa from the The ISME Journal 0 50000 100000 150000 200000 250000 300000 K in gd om P hy lu m C la ss O rd er F am ily G en us S pe ci es S eq ue nc es c la ss ifi ed to a t m os t.....
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"An improved Greengenes taxonomy wit..." refers methods in this paper
...A tree of the remaining 408 135 filtered sequences, (tree_16S_all_gg_2011_1) was built using FastTree v2....
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...Therefore, in order to address the classification of these groups we amended tree_16S_all_gg_2011_1 with 765 mostly partial length sequences from GenBank and generated a new de novo tree using FastTree; tree_16S_candiv_gg_2011_1....
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..., 2009), we constructed a phylogenetic tree using FastTree2 (Price et al., 2010) containing 408 135 sequences (tree_16S_all_gg_2011_1)....
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...For evaluation of NCBI-defined candidate phyla, we added 765 mostly partial length sequences, that failed the Greengenes filtering procedure but were required for the evaluation, to the alignment using PyNAST (Caporaso et al., 2010; based on the 29 November, 2010 Greengenes OTU templates) and generated a second FastTree (tree_16S_candiv_gg_ 2011_1) using the parameters described above....
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...The Greengenes taxonomy is currently based on a de novo phylogenetic tree of 408 135 quality-filtered sequences calculated using FastTree (Price et al., 2010)....
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