Comprehensive assessment of error correction methods for high-throughput sequencing data

Comprehensive assessment of error correction methods for high-throughput sequencing data

Yun Heo, Gowthami Manikandan, Anand Ramachandran, Deming Chen

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.

高通量测序数据误差校正方法的综合评估

DNA和RNA测序的出现彻底改变了基因组学和分子生物学的研究。
下一代测序(NGS)技术，如Illumina、Ion Torrent、SOLiD测序等，为基因组测序带来了快速、廉价的方法。
最近，第三代测序(TGS)技术如PacBio和Oxford Nanopore Technology (ONT)也被开发出来。
不同的技术使用不同的基本排序方法，容易出现不同的错误率。
虽然NGS和TGS方法对测序数据进行误差修正的工具很多，但是目前还没有标准的方法来评价这些误差修正工具的准确性和有效性。
在本研究中，我们提出了一个核酸序列纠错工具评估软件包(眼镜)，为NGS和TGS平台提供全面的算法来评估DNA和RNA测序的纠错方法。
我们还为Illumina、PacBio和ONT平台提供了测序数据集的汇编，为纠错工具提供了具有挑战性的场景。
使用这些数据集和眼镜，我们评估23种不同的错误纠正工具的性能，并提出独特和有益的见解，了解它们的优缺点。
我们希望我们的方法将来能使DNA和RNA的错误校正工具的评估标准化。