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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UCLUST article

UCLUST citations

 (6)
2017
PMCID: 5593928

[…] were clustered into operational taxonomic units (otus) using quantitative insights into microbial ecology (qiime)14 and the greengenes reference database15 and were taxonomically assigned with the uclust consensus taxonomy assigner16. to minimize risk of including false positive otus, we performed a series of filtering steps for analysis. first, we removed otus observed only once from samples […]

2017
PMCID: 5371072

[…] 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 […]

2016
PMCID: 5147981

[…] trimmed using a fastx_trimmer tool (http://hannonlab.cshl.edu/fastx_toolkit/) before assembling with the paired-end assembler [23]. otus were selected with ≥97% sequence identity cut-off using the uclust [24]. representative sequences of picked otus were aligned by pynast [25]. chimeric sequences were identified from the alignments by chimeraslayer [26]. taxonomy was assigned using blast […]

2016
PMCID: 4802634

[…] failed the first clustering were clustered against the new reference database generated in step 2; and (4) remaining unclassified sequences were clustered de novo. clustering was performed using uclust [31], and resulting sequences were aligned to greengenes with pynast [29]. otu classification was reported to the lowest possible taxonomic level., a dataset containing otus specific to hide […]

2016
PMCID: 4718982

[…] sequences. finally, otus that failed to align to any sequences in the reference database are de novo clustered. representative sequences from each otu were picked and assigned taxonomy using the uclust consensus taxonomy assigner. during this process, sequences with high identity (>97%) were grouped into the same otu, and are reported at the lowest level of taxonomic identification common […]

UCLUST institution(s)
Tiburon, CA, USA

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