QAlign: aligning nanopore reads accurately using current-level modeling

Author:

Joshi Dhaivat1,Mao Shunfu2,Kannan Sreeram2,Diggavi Suhas1

Affiliation:

1. Electrical & Computer Engineering, University of California, Los Angeles, CA 90095, USA

2. Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA

Abstract

Abstract Motivation Efficient and accurate alignment of DNA/RNA sequence reads to each other or to a reference genome/transcriptome is an important problem in genomic analysis. Nanopore sequencing has emerged as a major sequencing technology and many long-read aligners have been designed for aligning nanopore reads. However, the high error rate makes accurate and efficient alignment difficult. Utilizing the noise and error characteristics inherent in the sequencing process properly can play a vital role in constructing a robust aligner. In this article, we design QAlign, a pre-processor that can be used with any long-read aligner for aligning long reads to a genome/transcriptome or to other long reads. The key idea in QAlign is to convert the nucleotide reads into discretized current levels that capture the error modes of the nanopore sequencer before running it through a sequence aligner. Results We show that QAlign is able to improve alignment rates from around 80% up to 90% with nanopore reads when aligning to the genome. We also show that QAlign improves the average overlap quality by 9.2, 2.5 and 10.8% in three real datasets for read-to-read alignment. Read-to-transcriptome alignment rates are improved from 51.6% to 75.4% and 82.6% to 90% in two real datasets. Availability and implementation https://github.com/joshidhaivat/QAlign.git. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

National Science Foundation

National Institutes of Health

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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