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UPARSE specifications


Unique identifier OMICS_01449
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for UPARSE

UPARSE citations


Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial

PMCID: 5964358
DOI: 10.1128/mBio.02392-17
call_split See protocol

[…] less than 0.5. Operational taxonomic units (OTUs) were delineated at the cutoff of 97% using the USEARCH v.7.0.1090 pipeline. The protocol can be found on the website http://drive5.com/usearch/manual/uparse_pipeline.html. The detailed procures were stated in our previous publication (). α- and β-diversity analyses were performed using QIIME v1.8.0 (). To normalize read depth, all samples were rand […]


High‐throughput discovery of functional disordered regions: investigation of transactivation domains

Mol Syst Biol
PMCID: 5949888
PMID: 29759983
DOI: 10.15252/msb.20188190

[…] The sequencing read processing stage resembles metagenomics pipelines [e.g., UPARSE (Edgar, ) or vsearch (preprint: Rognes et al, )] with adjustments to parameters as described below. The sequences of the reads from the different samples (i.e., time points) were first combined […]


Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice

PMCID: 5949713
PMID: 29760543
DOI: 10.3748/wjg.v24.i18.1995
call_split See protocol

[…] a Kit combined with the HiSeq 2500 System (Illumina) sequencer, according to the manufacturer’s instructions. Sequence reads obtained from the V4 region of the 16S gene were analysed according to the UPARSE pipeline[], using the USEARCH v9.2.64 package. For OTU clustering a threshold of 97% similarity was used through the UPARSE-OTU algorithm. α- and β-diversity analyses were calculated using the […]


Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community

PMCID: 5946436
PMID: 29751830
DOI: 10.1186/s40168-018-0475-7

[…] 16S OTU clustering was performed using UPARSE (http://drive5.com/uparse/) []. Paired reads were merged and filtered at maximum expected error threshold of 1.0 (-fastq_maxee 1.0). Unique sequences were identified using the “fastx_uniques” c […]


Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

Sci Rep
PMCID: 5943461
PMID: 29743727
DOI: 10.1038/s41598-018-25760-7

[…] y clean tags. The tags were compared with the reference database (Gold Database) using UCHIME algorithm to detect chimera sequences, which were removed. The resulted effective tags were analyzed with Uparse software (V8.1.1861). Sequences with ≥97% similarity were assigned to the same operational taxonomic units (OTUs). Representative sequences for each OTU were screened for further annotation. Fo […]


Microbial diversity and ecotoxicity of sediments 3 years after the Jiaozhou Bay oil spill

PMCID: 5943202
PMID: 29744605
DOI: 10.1186/s13568-018-0603-6
call_split See protocol

[…] y controlled process (Caporaso et al. ; Bokulich et al. ). The effective tags were finally obtained after chimera removal (Edgar et al. ; Haas et al. ). Analyses of the sequences were performed using Uparse software (Uparse v7.0.1001) (Edgar ). Sequences with ≥ 97% similarity were assigned to the same OTUs. A representative sequence for each OTU was screened for further annotation with the Green G […]


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UPARSE institution(s)
Tiburon, CA, USA

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