USEARCH statistics

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Citations per year

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Popular tool citations

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Associated diseases


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USEARCH specifications


Unique identifier OMICS_05156
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





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  • person_outline Robert Edgar <>

Publications for USEARCH

USEARCH in pipelines

PMCID: 5749787
PMID: 29293587
DOI: 10.1371/journal.pone.0190351

[…] for phix using bowtie2 v2.2.1 [] and reconstituted into two fastq files for each read using standard bash. sequencing reads were merged, allowing 4 mismatches per ≥50 bases, then processed using usearch v7.0.1001 []. sequences were demultiplexed using qiime v1.8.0 [] and then clustered using the uparse pipeline []. operational taxonomic unit (otu) classification was accomplished by mapping […]

PMCID: 5759035
PMID: 29354144
DOI: 10.3389/fpls.2017.02191

[…] obtained after wotu clustering among the wells; supplementary figure and “sequencing and data processing” in supplementary methods ). the taxonomic prediction was assigned for cotus using “utax” in usearch v8.1 (edgar, ) and rdp (cole et al., ) database ( with a confidence score of 0.9., phylogenetic analysis was performed by multiple alignments of cotu sequences […]

PMCID: 5760547
PMID: 29354109
DOI: 10.3389/fmicb.2017.02624

[…] fastqc () revealed that only forward reads were useful for downstream analyses. sequences were de-multiplexed and processed using qiime () with a phred score of 20 and chimera filtering with the usearch61 hierarchical clustering method (). sequences were clustered into operational taxonomic units (otus) using uclust () with a 97% identity threshold. taxonomic assignment was performed using […]

PMCID: 5762663
PMID: 29321528
DOI: 10.1038/s41467-017-02535-8

[…] following schirmer et al.. corrected paired-end reads were subsequently merged with pear; sequences longer than 200 bp were quality-checked (maximum expected errors 0.5) and de-replicated using usearch. otu were delineated at 97% similarity using uparse v8.1.1756. to obtain otu abundances, reads were mapped back to otus at 97% similarity using an exhaustive search (-maxaccepts 20 […]

PMCID: 5766484
PMID: 29330469
DOI: 10.1038/s41598-017-18528-y

[…] the effect of examining duplicated and related genes, the coding regions of the down- and up-regulated genes were extracted from biomart as described above and compared using the metagenomic tool usearch ( no matches above 50% were found., the upstream regions of down- and up-regulated genes were searched for known transcription factor binding sites (tfbs) using […]

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USEARCH in publications

PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18

[…] 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 […]

PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] 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 […]

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

[…] 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)., the operation taxonomic units (otus) present at the species level were evaluated for their differential presence across the patient groups. […]

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

[…] 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 […]

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

[…] activity, we tracked their v4 hypervariable sequences in the total pool of v4 sequences in each corresponding holobiont microbiomes. we used different similarity identity thresholds using usearch tool from galaxy platform []. this tool is based on usearch and uclust algorithms []. these thresholds varied from 100% to 98.00%, i.e. from 0 to 5 different nucleotides in the sequences […]

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

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