UPARSE protocols

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


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Publication for UPARSE

UPARSE IN pipelines

PMCID: 5835065
PMID: 29535685
DOI: 10.3389/fmicb.2018.00280

[…] “split_library_fastq.py.” chimera sequences were identified and removed with uchime (edgar et al., 2011) against the gold database (bernal et al., 2001). otu formation was performed following the uparse pipeline (edgar, 2013) and the dereplicated reads were clustered into otus at a 97% sequence similarity threshold. singleton otus were removed and the remaining high-quality sequence reads […]

PMCID: 5288354
PMID: 28210252
DOI: 10.3389/fmicb.2017.00143

[…] (caporaso et al., 2010; bokulich et al., 2013). chimera sequences were detected by uchime algorithm and were removed (edgar, 2011). then, sequences were classified to otus at 97% similarity using uparse pipeline and representative sequence for each otu was screened (edgar, 2013). alpha diversity analyses including computation of the shannon, simpson, chao 1 indexes and coverage were used […]

PMCID: 5527301
PMID: 28761935
DOI: 10.1128/mSystems.00043-17

[…] and a minimum read length of 32 bp. the assembled sequences were analyzed by qiime (quantitative insights into microbial ecology) version 1.9.0 (54). the sequences were then clustered de novo with uparse (55) at 97% and 99% sequence identity, which also removed chimeras and sequences that appeared only once in the data set (55). the clustered sequences were then aligned with pynast version […]

PMCID: 5651609
PMID: 29058583
DOI: 10.1186/s12864-017-4215-3

[…] single sequence spanning the entire v1-v2 region [45]. sequences were then dereplicated and chimeric sequences removed using uchime [46]. operational taxonomic units (otus) were then generated using uparse [47] and taxonomic assignments were generated using the standalone rdpclassifier v2.6 [48, 49] with the default --minwords option of 5. tax4fun [50] was used to predict the functional […]

PMCID: 4589578
PMID: 26457297
DOI: 10.1155/2015/173729

[…] and population genetics studies. otu clustering is conducted to estimate the number of species or genera in each sample by applying a similarity threshold (97% in our study). to ensure accuracy, a uparse pipeline was used to cluster sequences into otus [18], and uchime was used to eliminate chimaeras among sequences [19]. to perform the taxonomic analysis, each otu was aligned to the silva […]

UPARSE institution(s)
Tiburon, CA, USA

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