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OTU analysis benchmarks and papers

Algorithm
 
Benchmark results Paper
Paired read merging (assembly) Paired read assembler validation Edgar & Flyvbjerg (2015) Error filtering, pair assembly and error correction for next-generation sequencing reads.
 
Quality filtering by expected errors. Read quality filtering validation Edgar & Flyvbjerg (2015) Error filtering, pair assembly and error correction for next-generation sequencing reads.
 
Taxonomy prediction Taxonomy benchmarks (Paper in submission).
 
OTU clustering with simultaneous chimera filtering. OTU benchmarks Edgar (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads.
 
Stand-alone chimera filtering
 
Chimera benchmarks Edgar et al. (2011) UCHIME improves sensitivity and speed of chimera detection.