<<<<<<< .mine UPARSE OTU clustering
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UPARSE has been cited by
219 papers
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Last updated 31 Jul 2015
 
 
 
 
 
USEARCH  


High-accuracy, high-throughput OTU clustering
UPARSE is a method for generating clusters (OTUs) from next-generating sequencing reads of marker genes such as 16S rRNA, the fungal ITS region and the COI gene. The clustering method itself is the UPARSE-OTU algorithm, implemented as the cluster_otus command in USEARCH. To run UPARSE in practice, you need to run a pipeline of scripts and USEARCH commands.

Benchmark tests
According to results published in Nature Methods, UPARSE generates OTUs that are far superior to state-of-the-art methods including QIIME, mothur and AmpliconNoise on mock community tests. OTU representative sequences are more accurate predictions of biological sequences, and the number of OTUs are much closer to the number of species.


Reference
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772dx.doi.org/10.1038/nmeth.2604].
 
 

======= UPARSE OTU clustering
Home Software Services About Contact
 
UPARSE has been cited by
219 papers
Google scholar
Last updated 31 Jul 2015
 
 
 
 
 
USEARCH  


High-accuracy, high-throughput OTU clustering
UPARSE is a method for generating clusters (OTUs) from next-generating sequencing reads of marker genes such as 16S rRNA, the fungal ITS region and the COI gene. The clustering method itself is the UPARSE-OTU algorithm, implemented as the cluster_otus command in USEARCH. To run UPARSE in practice, you need to run a pipeline of scripts and USEARCH commands.

Benchmark tests
According to results published in Nature Methods, UPARSE generates OTUs that are far superior to state-of-the-art methods including QIIME, mothur and AmpliconNoise on mock community tests. OTU representative sequences are more accurate predictions of biological sequences, and the number of OTUs are much closer to the number of species.


Reference
Edgar, R.C. (2013) UPARSE: Highly accurate OTU sequences from microbial amplicon reads, Nature Methods [Pubmed:23955772dx.doi.org/10.1038/nmeth.2604].
 
 

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