UPARSE specifications

Information


Unique identifier OMICS_01449
Name UPARSE
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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UPARSE article

UPARSE citations

 (2)
2018
PMCID: 5918619

[…] rate of 0.05. illumina phix control sequences were removed with bowtie2 [36]. all remaining sequences were subsequently clustered into operational taxonomic units (otus), with chimera removal using uparse [37]. taxonomy assignment was performed closed-reference against the silva database (release 123) at 97% identity, resulting in 7,083,883 total reads (median 18,190 reads/sample). samples […]

2015
PMCID: 4817673

[…] under accession numbers 4571868.3–4571924.3 and project number 10023., paired end reads were quality trimmed and processed for operational taxonomic unit (otu) clustering using uparse pipeline (edgar, 2013), set at 0.97% identity cutoff. taxonomic status was assigned to the high-quality (<1% incorrect bases) candidate otus using the ‘parallel_assign_taxonomy_rdp.py' […]

UPARSE institution(s)
Tiburon, CA, USA

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