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proovread: large-scale high-accuracy PacBio correction through iterative short read consensus.

Thomas Hackl¹, Rainer Hedrich², Jörg Schultz²

¹Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany and Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany.

Bioinformatics (Oxford, England)

|July 13, 2014

Summary

proovread is a new pipeline that corrects errors in long-read single molecule real-time (SMRT) sequencing data. This method improves accuracy and throughput, making SMRT sequencing more valuable for large projects.

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Area of Science:

Genomics and Bioinformatics
Molecular Biology

Background:

Illumina sequencing by synthesis yields accurate but short DNA reads.
Single molecule real-time (SMRT) sequencing offers long reads but suffers from high error rates.
Current hybrid correction methods for SMRT reads are resource-intensive and have limitations.

Purpose of the Study:

To develop a flexible and efficient hybrid correction pipeline for SMRT sequencing data.
To improve the accuracy and usability of long-read sequencing technologies.
To enhance the application of SMRT sequencing in large-scale genomic and transcriptomic projects.

Main Methods:

Developed proovread, a hybrid correction pipeline for single molecule real-time (SMRT) reads.
Designed for flexible adaptation to various hardware and computing infrastructures.
Tested on genomic and transcriptomic datasets from Escherichia coli, Arabidopsis thaliana, and human.

Main Results:

Achieved accuracies up to 99.9% on test cases.
Outperformed existing hybrid correction programs in accuracy and throughput.
Produced longer corrected sequences and higher overall throughput.
Demonstrated adaptability from laptops to high-performance computing clusters.

Conclusions:

proovread offers highly accurate correction of SMRT reads with excellent hardware adaptability.
The pipeline significantly increases the applicability and value of SMRT sequencing data.
proovread is a valuable tool for large sequencing projects requiring long-read accuracy.