UCHIME vs. UPARSE

See also
Chimera benchmark home
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.