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Protocols

USEARCH specifications

Information


Unique identifier OMICS_05156
Name USEARCH
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 10.0.240
Stability Stable
Maintained Yes

Subtool


  • UNOISE

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Versioning


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Documentation


Maintainer


  • person_outline Robert Edgar

Publications for USEARCH

USEARCH citations

 (1506)
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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

2018
MBio
PMCID: 5964358
DOI: 10.1128/mBio.02392-17
call_split See protocol

[…] read. (iii) These reads were not kept unless they were longer than 399 bp and the expected errors were 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- […]

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Food Starch Structure Impacts Gut Microbiome Composition

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

[…] ta were analyzed by Quantitative Insight Into Microbial Ecology (QIIME) version 1.9.1 (). Sequences with a Phred score of lower than 20 were removed. Chimeric sequences were checked 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 […]

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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

[…] ns were pooled and ligated to Illumina adaptors. Sequencing was performed on a single lane on an Illumina MiSeq instrument (paired-end reads). The forward and reverse read pairs were merged 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 d […]

library_books

Linking cervicovaginal immune signatures, HPV and microbiota composition in cervical carcinogenesis in non Hispanic and Hispanic women

2018
Sci Rep
PMCID: 5954126
PMID: 29765068
DOI: 10.1038/s41598-018-25879-7

[…] he V4 region of bacterial 16S rRNA operon was amplified from the genomic DNA obtained from vaginal swabs and sequenced on the MiSeq platform (Illumina, San Diego, CA). The samples were analyzed using USEARCH (for details see Supplementary Methods). […]

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

2018
PMCID: 5949713
PMID: 29760543
DOI: 10.3748/wjg.v24.i18.1995
call_split See protocol

[…] 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 R package Phyloseq v.1.19.1[] […]

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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

[…] d homopolymers, and chimeric sequences. The sequences were then clustered into operational taxonomic units (OTUs) with a 97% similarity cutoff () with the 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 defaul […]

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USEARCH institution(s)
Department of Micro- and Nanotechnology, Technical University of Denmark, Lyngby, Denmark

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