UCLUST 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

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Publication for UCLUST

UCLUST IN pipelines

 (18)
2018
PMCID: 5768916
PMID: 29375529
DOI: 10.3389/fmicb.2017.02667

[…] 1.9.1) (caporaso et al., 2010b). open-reference otu picking was performed using the sortmerna (version 2.0) method (kopylova et al., 2012) with a minimum identity of 97%. taxonomy was assigned using uclust (version 1.2.22) (edgar, 2010) with the greengenes database as reference (version 13.8) and sequences were aligned using pynast (version 1.2.2) (caporaso et al., 2010a). otu’s identified […]

2018
PMCID: 5826226
PMID: 29515550
DOI: 10.3389/fmicb.2018.00270

[…] reads (q<25), and reads of < 400 bp in length were removed. reads were assigned to operational taxonomic units using the pick_open_reference_otus.py command with default parameters using the uclust method (edgar, 2010). otus occurring only once (singletons) or that failed to align using pynast were removed (caporaso et al., 2010a). relative diversity analyses were generated using […]

2017
PMCID: 5317032
PMID: 28218290
DOI: 10.1038/srep42625

[…] a conservative chimera detection filter using the chimeraslayer method60. selected high quality chimera–free sequences were clustered into operational taxonomic units (otus) within reads using the uclust61 with a pairwise identity threshold of 0.97., representative sequences for each otu were picked using the “most–abundant” method and otu sequence alignment was performed with pynast59. […]

2017
PMCID: 5371072
PMID: 28302989
DOI: 10.1264/jsme2.ME16158

[…] of reads was evaluated using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)., 16s rrna sequences were sorted into otus with a criterion of 97% sequence identity using the program uclust implemented in the qiime v1.8.0 package with the furthest-neighbor clustering algorithm (6, 12). chimeric sequences were identified using uchime (13), and singletons were also eliminated […]

2017
PMCID: 5383679
PMID: 28108915
DOI: 10.1007/s11356-017-8377-y

[…] their barcode sequence. the number of sequences presents before and after quality filtering is shown in online resource 9. clustering into operational taxonomic units (otus) was then performed using uclust at the 97% similarity level, indicative of species level (edgar 2010). the most abundant sequences were chosen as being representative of a cluster and aligned with the pynast method (caporaso […]

UCLUST institution(s)
Tiburon, CA, USA

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