SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

By Evguenia Kopylova, Laurent Noé, H. Touzet. Bioinform., 2012

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View Paper: https://www.semanticscholar.org/paper/c2240cddc8ad8d06b6e7c36eae4bfef027bf8ca2

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In Molecular Biology

Citations in the corpus

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research (2017, neutral): “0-dev time stamped 29/11/2014 [39]) and SUMACLUST (v1.”
IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies (2016, positive): “Non-prokaryotic OTUs ( e.g. , phiX or eukaryotic contaminations) are filtered out using SortmeRNA 35 (version 2.0), and the final OTU list is used to map filtered reads and build an OTU table with relative sequence abundance for each sample.”
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information (2018, result): “We contrast this performance with that of SortMeRNA (24), a purely sequence-based representative of the closed-reference approach.”
Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study (2020, methodology): “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.”
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest (2015, methodology): “Putative rRNAs in the remaining sequences were identified using SortMeRNA (Kopylova et al., 2012) with the non-redundant version of the following databases: rfam 5.8S (version 11.0) (Burge et al., 2013); Unite25 (November 2011 version) (Kõljalg et al., 2013), and Silva 18S and Silva 28S…”
A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle (2019, neutral): “9 (26) using all 110 included databases.”
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease (2016, neutral): “…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…”
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin (2018, methodology): “0 29/11/2014) 108 [15]), two alignment-based consensus taxonomy classifiers newly released in q2-feature109 classifier (based on BLAST+ (version 2.”