  The advent of DNA and RNA sequencing has revolutionized the study of genomics
and molecular biology. Next generation sequencing (NGS) technologies like
Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and
cheap way to sequence genomes. Recently, third generation sequencing (TGS)
technologies like PacBio and Oxford Nanopore Technology (ONT) have also been
developed. Different technologies use different underlying methods for
sequencing and are prone to different error rates. Though many tools exist for
error correction of sequencing data from NGS and TGS methods, no standard
method is available yet to evaluate the accuracy and effectiveness of these
error-correction tools. In this study, we present a Software Package for Error
Correction Tool Assessment on nuCLEic acid sequences (SPECTACLE) providing
comprehensive algorithms to evaluate error-correction methods for DNA and RNA
sequencing, for NGS and TGS platforms. We also present a compilation of
sequencing datasets for Illumina, PacBio and ONT platforms that present
challenging scenarios for error-correction tools. Using these datasets and
SPECTACLE, we evaluate the performance of 23 different error-correction tools
and present unique and helpful insights into their strengths and weaknesses. We
hope that our methodology will standardize the evaluation of DNA and RNA
error-correction tools in the future.
