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SINTAX specifications


Unique identifier OMICS_23523
Alternative name SImple Non-Bayesian TAXonomy

Publication for SImple Non-Bayesian TAXonomy

SINTAX citations


Bacterial Microbiome Dynamics in Post Pull Through Hirschsprung Associated Enterocolitis (HAEC): An Experimental Study Employing the Endothelin Receptor B Null Mouse Model

PMCID: 5897423
PMID: 29682507
DOI: 10.3389/fsurg.2018.00030
call_split See protocol

[…] ainst the nt database. OTUs were removed if any of their highest scoring BLAST hits contained taxonomic IDs within the family Rodents or to PhiX. Taxonomic assignments to the OTUs were performed with SINTAX () using RDP Classifier 16S training set number 16 () as the reference database. […]


Insights into microbial communities mediating the bioremediation of hydrocarbon contaminated soil from an Alpine former military site

Appl Microbiol Biotechnol
PMCID: 5932094
PMID: 29594357
DOI: 10.1007/s00253-018-8932-6

[…] o taxa by using the RDP classifier (Wang et al. ) against the UNITE database with a 50% confidence threshold, as previously reported (Barberan et al. ; Siles and Margesin ); and although other tools (sintax command of USEARCH pipeline) and training sets (WARCUP (Deshpande et al. )) were also applied to try to improve the proportion of classified reads, similar rates of classified sequences were ob […]


Resuscitation of viable but non‐culturable bacteria to enhance the cellulose‐degrading capability of bacterial community in composting

PMCID: 5902322
PMID: 29536669
DOI: 10.1111/1751-7915.13256
call_split See protocol

[…] similarity cut‐off using USEARCH UPARSE (Edgar, ), and the chimeric sequences were removed in the UPARSE pipeline. The phylogenetic affiliation of each 16S rRNA gene sequence was analysed by USEARCH SINTAX algorithm against the Ribosomal Database Project (RDP) 16S rRNA gene training set (version 16) using confidence threshold of 0.8. The OTUs identified as mitochondrial or chloroplast rRNA sequen […]


A Community Based Culture Collection for Targeting Novel Plant Growth Promoting Bacteria from the Sugarcane Microbiome

Front Plant Sci
PMCID: 5759035
PMID: 29354144
DOI: 10.3389/fpls.2017.02191
call_split See protocol

[…] The OTUs from inoculated and uninoculated plants were identified using SINTAX (Edgar, ) in USEARCH v9.2 and the SINTAX-compatible SILVA 16S rRNA gene database ( The Bray–Curtis dissimilarity matrix was calculated and employed f […]


Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Ecol Evol
PMCID: 5756863
PMID: 29321862
DOI: 10.1002/ece3.3638

[…] lity filtering (maxee setting of 0.5), PHiX and chimera removal, and OTU (Operational Taxonomic Unit) clustering were implemented via the UNOISE (v2) pipeline (Edgar, ). Taxonomy was assigned via the SINTAX approach (described below) implemented in USEARCH (Edgar, , ). As the primers and blocking primer were optimized for the detection metazoan taxa, any OTUs that were not classified to a metazoan […]


From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept

Front Microbiol
PMCID: 5420814
PMID: 28533770
DOI: 10.3389/fmicb.2017.00821

[…] s at databases, such as GreenGenes (for bacteria community characterization), SILVA (bacteria and eucaryotes) and Unite (for Fungi) among others. Again, a range of software is available (Qiime, UTAX, SINTAX, stampa) (; , ). This stage is again a source of biases, partly because OTUs can represent multiple species, there is ambiguous assignment, and because too small differences that do exist could […]


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SINTAX institution(s)
Tiburon, CA, USA

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