title: DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences.
abstract: DECIPHER is a new method for finding 16S rRNA chimeric sequences by the use of a search-based approach. The method is based upon detecting short fragments that are uncommon in the phylogenetic group where a query sequence is classified but frequently found in another phylogenetic group. The algorithm was calibrated for full sequences (fs_DECIPHER) and short sequences (ss_DECIPHER) and benchmarked against WigeoN (Pintail), ChimeraSlayer, and Uchime using artificially generated chimeras. Overall, ss_DECIPHER and Uchime provided the highest chimera detection for sequences 100 to 600 nucleotides long (79% and 81%, respectively), but Uchime's performance deteriorated for longer sequences, while ss_DECIPHER maintained a high detection rate (89%). Both methods had low false-positive rates (1.3% and 1.6%). The more conservative fs_DECIPHER, benchmarked only for sequences longer than 600 nucleotides, had an overall detection rate lower than that of ss_DECIPHER (75%) but higher than those of the other programs. In addition, fs_DECIPHER had the lowest false-positive rate among all the benchmarked programs (<0.20%). DECIPHER was outperformed only by ChimeraSlayer and Uchime when chimeras were formed from closely related parents (less than 10% divergence). Given the differences in the programs, it was possible to detect over 89% of all chimeras with just the combination of ss_DECIPHER and Uchime. Using fs_DECIPHER, we detected between 1% and 2% additional chimeras in the RDP, SILVA, and Greengenes databases from which chimeras had already been removed with Pintail or Bellerophon. DECIPHER was implemented in the R programming language and is directly accessible through a webpage or by downloading the program as an R package (http://DECIPHER.cee.wisc.edu).
authors.affiliation: Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Erik S
authors.initials: ES
authors.lastname: Wright
authors.forename: L Safak
authors.initials: LS
authors.lastname: Yilmaz
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Noguera
mesh_terms: D002678:Chimera; D019295:Computational Biology / Q000379:methods*; D003951:Diagnostic Errors; D020459:Genes, rRNA; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity
chemical_list: D012336:RNA, Ribosomal, 16S
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