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Protocols

Greengenes specifications

Information


Unique identifier OMICS_26865
Name Greengenes
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Content license CC Attribution-NonCommercial-ShareAlike
Maintained Yes

Maintainer


  • person_outline Gary Andersen

Greengenes citations

 (1942)
call_split

Food Starch Structure Impacts Gut Microbiome Composition

2018
PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18
call_split See protocol

[…] d and removed using USEARCH version 6.1.544 (). The remaining high-quality reads were clustered into operational taxonomic units (OTUs) by PyNAST () with a 97% sequence identity threshold against the Greengenes core set database version 13.8 (). The generated biome table was normalized using an equal subsampling size of 2,938 sequences. Distances between bacterial communities in different samples […]

library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] ncing round in the American Gut used 125 cycles while the rest used 150. Following processing by Deblur, previously recognized bloom sequences were removed (). The Deblur sOTUs were inserted into the Greengenes 13_8 () 99% reference tree using SEPP (). SEPP uses the simultaneous alignment and tree estimation strategy described in reference to identify reasonable placements for sequence fragments […]

call_split

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

2018
mSystems
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17
call_split See protocol

[…] d using the USEARCH v7 program fastq_mergepairs, allowing stagger but no mismatches (). Operational taxonomic units (OTUs) were picked using the closedreference picking script in QIIME v1.7.0 and the Greengenes database (August 2013 release) (). The similarity threshold was set at 97%, reverse read matching was enabled, and reference-based chimera calling was disabled. The unfiltered OTU table use […]

library_books

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome resolved metagenomics

2018
Biotechnol Biofuels
PMCID: 5946492
PMID: 29774049
DOI: 10.1186/s13068-018-1136-6

[…] clustered at 97% identity for 80 iterations. Reconstructed 16S rRNA gene sequences (> 1200 bp) post-chimera checking using ChimeraSlayer were annotated by BLASTN search against both SILVA SSU 115 and GreenGenes (2013–5 release) databases at an e value of 1e−20. The relative abundance of each 16S rRNA gene sequences was calculated by EMIRGE based on the length-normalized read number of mapped reads […]

library_books

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes

2018
PLoS One
PMCID: 5942802
PMID: 29742123
DOI: 10.1371/journal.pone.0196178

[…] f V4 sequences was ∼252 bp. For quality filtering, QIIME default parameters were used, with a minimun Phred quality score <20 and ambiguous nucleotides were removed. Sequence alignment was made using Greengenes database [] and PyNast alignment algorithm []. UCLUST software [] was used to assign similar sequences to operational taxonomic units (OTUs) by clustering sequences based on a 97% similarit […]

library_books

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild Type Salmonella enterica Serovar Typhi

2018
MBio
PMCID: 5941076
PMID: 29739901
DOI: 10.1128/mBio.00686-18

[…] rational taxonomic units (OTUs) based on a 97% cutoff with USEARCH. Taxonomic ranks were assigned to each sequence with the Ribosomal Database Project (RDP) Naive Bayesian Classifier v.2.2, using the Greengenes database of 16S rRNA gene sequences (August 2013) and a confidence value cutoff of 0.97. […]

Citations

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Greengenes institution(s)
Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Microbial Ecology Program, DOE Joint Genome Institute, Walnut Creek, CA, USA; Danish Genome Institute, Aarhus, Denmark; Department of Bioinformatics, Baylor University, Waco, TX, USA; Department of Bioengineering, University of California, Berkeley, CA, USA; Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, QLD, Australia; Department of Computer Science, Chalmers University of Technology, Goteborg, Sweden
Greengenes funding source(s)
Supported in part by the Department of Homeland Security under grant HSSCHQ04X00037.

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