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UPARSE-OTU algorithm with chimera filtering (cluster_otus command).
UCHIME and UPARSE compared for OTU clustering
Below is Fig 1(a) from the UPARSE paper. Magenta segments in the pie chart show the fraction of chimeric OTUs generated by several algorithms on a mock community test. The QIIME and mothur pipelines used UCHIME for chimera detection. Notice that even after UCHIME filtering, about 50% of the OTUs generated by QIIME and mothur are chimeric, while UPARSE successfully filters all chimeras from Illumina reads and leaves only one chimeric OTU with 454 reads.