DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

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 (fsDECIPHER) and short sequences (ssDECIPHER) and benchmarked against WigeoN (Pintail), ChimeraSlayer, and Uchime using artificially generated chimeras. Overall, ssDECIPHER 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 ssDECIPHER maintained a high detection rate (89%). Both methods had low false-positive rates (1. 3% and 1. 6%). The more conservative fsDECIPHER, benchmarked only for sequences longer than 600 nucleotides, had an overall detection rate lower than that of ssDECIPHER (75%) but higher than those of the other programs. In addition, fsDECIPHER 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 ssDECIPHER and Uchime. Using fsDECIPHER, 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).