Efficiency of PacBio long read correction by 2nd generation Illumina sequencing

Area of Science:

• Genomics
• Bioinformatics
• Sequencing Technology

Background:

• Long sequencing reads (e.g., PacBio) enable complex genome analysis but often lack quality.
• Enhancing long read quality is essential for downstream genomic and transcriptomic studies.
• Second-generation sequencing data offers a cost-effective method for long read correction.

Purpose of the Study:

• To evaluate universal programs for correcting long sequencing reads.
• To identify the optimal method for improving both the size and quality of long reads.
• To assess the performance and potential drawbacks of different long read correction tools.

Main Methods:

• Designed a dedicated testing procedure to evaluate long read correction programs.
• Selected universal software applicable to long read correction.
• Utilized high-quality second-generation sequencing data for read correction.

Main Results:

• HALC demonstrated superior performance in correcting PacBio long reads, optimizing both read size and quality.
• Tested correction tools exhibited unexpected behaviors, including read trimming and fragmentation.
• The corrected sequences are suitable for subsequent genomic and transcriptomic analyses.

Conclusions:

• HALC is the recommended tool for correcting PacBio long reads when size and quality are paramount.
• Careful consideration of potential side effects like fragmentation is necessary when selecting correction tools.
• Integrating second-generation data provides a viable strategy for enhancing long read accuracy.