SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Citations
2,475 citations
Cites background or methods from "SortMeRNA: Fast and accurate filter..."
...0 29/11/2014) [13]), two alignmentbased consensus taxonomy classifiers newly released in q2-...
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...First, we compare the q2-feature-classifier methods to the classifiers that have been most commonly used for classification of 16S rRNA and ITS marker-gene amplicon sequences accessed through QIIME 1 (RDP, BLAST, uclust, SortMeRNA)....
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...Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data....
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...Species-level classifications of 16S rRNA gene simulated sequences were best with optimized UCLUST and SortMeRNA configurations for V4 domain, and naive Bayes and RDP for V1–3 domain and full-length 16S rRNA gene sequences (Fig....
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...We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data....
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2,142 citations
Cites background or methods from "SortMeRNA: Fast and accurate filter..."
...…and Algorithms ImageJ National Institutes of Health https://imagej.nih.gov/ij/ Imaris Bitplane http://www.bitplane.com/imaris/imaris SortMeRNA 2.0 Kopylova et al. (2012) http://bioinfo.lifl.fr/RNA/sortmerna/ Greengenes Lawrence Berkeley National Labs…...
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...Operational Taxonomic Units (OTUs) were picked closed reference using SortMeRNA 2.0 (Kopylova et al., 2012) against the August 2013 release of Greengenes (McDonald et al., 2012) in QIIME 1.9 (Caporaso et al., 2010)....
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1,676 citations
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999 citations
Cites methods from "SortMeRNA: Fast and accurate filter..."
...1b).([14]) Taxonomic assignment of the clean reads was performed with Kraken 2 against the reference databases, including archaea, bacteria, fungi, human, plasmid, protozoa, univec, and virus sequences (software 2....
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References
88,255 citations
"SortMeRNA: Fast and accurate filter..." refers background or methods in this paper
...Received on May 16, 2012; revised on September 17, 2012; accepted on October 9, 2012...
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...The 16S rRNA database was used by SortMeRNA, riboPicker, BLASTN and SSU-ALIGN, and the 23S rRNA database was used by SortMeRNA, riboPicker and BLASTN....
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43,862 citations
"SortMeRNA: Fast and accurate filter..." refers background or methods in this paper
...Received on May 16, 2012; revised on September 17, 2012; accepted on October 9, 2012...
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...An alternative algorithm outside the domain of probabilistic models is riboPicker (Schmieder et al., 2012), which uses a modified version of the Burrows-Wheeler Aligner (Li and Durbin, 2009)....
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"SortMeRNA: Fast and accurate filter..." refers background in this paper
...Additionally, the user can work with his or her own RNA databases....
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5,733 citations