A comprehensive evaluation of long read error correction methods
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RESEARCH
Open Access
A comprehensive evaluation of long read error correction methods Haowen Zhang1 , Chirag Jain1 and Srinivas Aluru1,2* From 8th IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS 2018) Las Vegas, NV, USA. 18-20 October 2018
Abstract Background: Third-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstream analysis. This difficulty has motivated the development of many long read error correction tools, which tackle this problem through sampling redundancy and/or leveraging accurate short reads of the same biological samples. Existing studies to asses these tools use simulated data sets, and are not sufficiently comprehensive in the range of software covered or diversity of evaluation measures used. Results: In this paper, we present a categorization and review of long read error correction methods, and provide a comprehensive evaluation of the corresponding long read error correction tools. Leveraging recent real sequencing data, we establish benchmark data sets and set up evaluation criteria for a comparative assessment which includes quality of error correction as well as run-time and memory usage. We study how trimming and long read sequencing depth affect error correction in terms of length distribution and genome coverage post-correction, and the impact of error correction performance on an important application of long reads, genome assembly. We provide guidelines for practitioners for choosing among the available error correction tools and identify directions for future research. Conclusions: Despite the high error rate of long reads, the state-of-the-art correction tools can achieve high correction quality. When short reads are available, the best hybrid methods outperform non-hybrid methods in terms of correction quality and computing resource usage. When choosing tools for use, practitioners are suggested to be careful with a few correction tools that discard reads, and check the effect of error correction tools on downstream analysis. Our evaluation code is available as open-source at https://github.com/haowenz/LRECE. Keywords: Long read, Error correction, Benchmark, Evaluation
Background Third-generation sequencing technologies produce long reads with average length of 10 Kbp or more that are orders of magnitudes longer than the short reads available through second-generation sequencing technologies (typically a few hundred bp). In fact, the longest read *Correspondence: [email protected] School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA 2 Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, GA 30332, USA 1
length reported to date is > 1 million bp [1]. Longer lengths are attractive because they enable disambiguation of repetitive regions in a genome or a set of genomes. The impact of this valuable long-r
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