UCLUST statistics

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Citations per year

Number of citations per year for the bioinformatics software tool UCLUST
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Tool usage distribution map

This map represents all the scientific publications referring to UCLUST per scientific context
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Associated diseases

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Protocols

UCLUST specifications

Information


Unique identifier OMICS_01448
Name UCLUST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for UCLUST

UCLUST citations

 (1532)
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

[…] efault 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% similarity threshold. The taxonomic assignment was achieved in diff […]

call_split

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

2018
PMCID: 5956146
PMID: 29743201
DOI: 10.1128/mSphere.00122-18
call_split See protocol

[…] pick_open_reference_otus.py script using the USEARCH algorithm v6.1544 against the SILVA reference data set version 128 (). Representative sequences for each OTU were taxonomically assigned using the UCLUST-based consensus classifier with default settings (). OTUs that were classified to the Archaea phylum were filtered from the OTU table and normalized to 1,000 sequences per sample. α and β diver […]

library_books

Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

2018
Microbiome
PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…]  nt) were analyzed with QIIME 1.9.1 [] using the Oracle VM VirtualBox version 5.0.26 r108824. Operational taxonomic units (OTUs) were picked using the two-step open-reference picking method using the UCLUST algorithm [], as implemented in QIIME using the pick_open_reference_otus.py command. Default settings were used, with the exception of picking OTUs at 99% similarity and training the RDP classi […]

library_books

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare

2018
Sci Rep
PMCID: 5934373
PMID: 29725059
DOI: 10.1038/s41598-018-25450-4

[…] iconNoise, and chimeras were removed using Perseus. All reads shorter than 250 bp were discarded and the remaining reads were clustered into Operational Taxonomic Units (OTUs) at 97% similarity using uclust. Representative sequences were aligned against the Silva reference alignment (release 108,) using PyNAST and identified using the RDP Classifier. Rare OTUs (i.e. singletons and doubletons) were […]

library_books

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

2018
Front Microbiol
PMCID: 5943533
PMID: 29774020
DOI: 10.3389/fmicb.2018.00887

[…] TU assignment, alpha diversity, and beta diversity calculations, were subsequently completed using the QIIME software package (). OTUs were defined at the identity levels of 80, 90, 95, and 97% using UCLUST () based on nucleotide sequences. The first sequence within each OTU cluster was picked as a representative sequence. The representative sequences were aligned with MUSCLE and used to construct […]

call_split

Killing Effects of an Isolated Serratia marcescens KH 001 on Diaphorina citri via Lowering the Endosymbiont Numbers

2018
Front Microbiol
PMCID: 5938409
PMID: 29765368
DOI: 10.3389/fmicb.2018.00860
call_split See protocol

[…] mplemented for Bioinformatics analysis (). Briefly, 16S rRNA operational taxonomic units (OTUs) were clustered using an open-reference OTU picking protocol based on 97% nucleotide similarity with the UCLUST algorithm (), and ChimeraSlayer was applied to remove chimeric sequences (). The relative abundance of each OTU was determined as a proportion of the sum of sequences for every sample, taxonomi […]


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UCLUST institution(s)
Tiburon, CA, USA

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