Abstract
BackgroundLong-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. However, the computation of the long sequencing reads is challenged by their higher error rates (e.g., 13% vs. 1%) and higher cost ($0.3 vs. $0.03 per Mbp) compared to the short reads.MethodsIn this paper, we present a new hybrid error correction tool, called ParLECH (Parallel Long-read Error Correction using Hybrid methodology). The error correction algorithm of ParLECH is distributed in nature and efficiently utilizes the k-mer coverage information of high throughput Illumina short-read sequences to rectify the PacBio long-read sequences.ParLECH first constructs a de Bruijn graph from the short reads, and then replaces the indel error regions of the long reads with their corresponding widest path (or maximum min-coverage path) in the short read-based de Bruijn graph. ParLECH then utilizes the k-mer coverage information of the short reads to divide each long read into a sequence of low and high coverage regions, followed by a majority voting to rectify each substituted error base.ResultsParLECH outperforms latest state-of-the-art hybrid error correction methods on real PacBio datasets. Our experimental evaluation results demonstrate that ParLECH can correct large-scale real-world datasets in an accurate and scalable manner. ParLECH can correct the indel errors of human genome PacBio long reads (312 GB) with Illumina short reads (452 GB) in less than 29 h using 128 compute nodes. ParLECH can align more than 92% bases of an E. coli PacBio dataset with the reference genome, proving its accuracy.ConclusionParLECH can scale to over terabytes of sequencing data using hundreds of computing nodes. The proposed hybrid error correction methodology is novel and rectifies both indel and substitution errors present in the original long reads or newly introduced by the short reads.
Highlights
Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly
We demonstrate the scalability of Parallel long-read error correction using hybrid methodology (ParLECH) by correcting a 312GB human genome PacBio dataset, with leveraging a 452 Giga bytes (GB) Illumina dataset (64x coverage), on 128 nodes in less than 29 h
Datasets We evaluate ParLECH with respect to four real data sets including E. coli, yeast, fruit fly, and human genome
Summary
Long-read sequencing has shown the promises to overcome the short length limitations of second-generation sequencing by providing more complete assembly. The second-generation sequencing technologies (e.g., Illumina, Ion Torrent) have been providing researchers with the required throughput at significantly low cost ($0.03/million-bases), which enabled the discovery of many new species and variants. They are being widely utilized for understanding the complex phenotypes, they are typically incapable of resolving long repetitive elements, common in various genomes (e.g., eukaryotic genomes), because of the short read lengths [1]. The production costs of these long sequences are almost 10 times more expensive than those of the short reads, and the analysis of these long reads is severely constrained by their higher error rate
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