Jul 11, 2018

Bi-level error correction for PacBio long reads

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Yuansheng LiuJinyan Li

Abstract

The latest sequencing technologies such as the Pacific Biosciences (PacBio) and Oxford Nanopore machines can generate long reads at the length of thousands of nucleic bases which is much longer than the reads at the length of hundreds generated by Illumina machines. However, these long reads are prone to much higher error rates, for example 15%, making downstream analysis and applications very difficult. Error correction is a process to improve the quality of sequencing data. Hybrid correction strategies have been recently proposed to combine Illumina reads of low error rates to fix sequencing errors in the noisy long reads with good performance. In this paper, we propose a new method named Bicolor, a bi-level framework of hybrid error correction for further improving the quality of PacBio long reads. At the first level, our method uses a de Bruijn graph-based error correction idea to search paths in pairs of solid -mers iteratively with an increasing length of -mer. At the second level, we combine the processed results under different parameters from the first level. In particular, a multiple sequence alignment algorithm is used to align those similar long reads, followed by a voting algorithm which determines the final base a...Continue Reading

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Mentioned in this Paper

Severe Acute Respiratory Syndrome
Positioning Attribute
Genome
Nucleic Acid Sequencing
Cell Nucleus
Cocaine
Sequencing
Downstream
Analysis
Nucleic Acids

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