FMLRC: Hybrid long read error correction using an FM-index.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Long read sequencing offers improved genome assembly continuity and accuracy despite high error rates.
• Current long read technologies face limitations in cost and throughput for complex genomes.
• Hybrid assembly strategies, using long reads for scaffolding and short reads for accuracy, present a potential solution.

Purpose of the Study:

• To develop and evaluate a novel hybrid method for correcting long read sequencing errors.
• To improve the efficiency and accuracy of de novo genome assembly using long and short reads.
• To enhance the economic viability of long read sequencing technologies.

Main Methods:

• A novel method employing a multi-string Burrows-Wheeler Transform with an auxiliary FM-index was developed.
• The method corrects errors in long reads by utilizing complementary short read data.
• Performance was evaluated against existing hybrid error-correction and de novo assembly methods.

Main Results:

• The novel method efficiently produces high-quality corrected long reads, surpassing existing hybrid approaches.
• Resulting de novo assemblies exhibit significantly improved contiguity compared to state-of-the-art methods.
• Increased throughput of corrected long reads was demonstrated.

Conclusions:

• The developed method accurately corrects long read sequence data using short reads.
• The approach leads to more contiguous de novo assemblies with higher throughput.
• Improved computational efficiency and throughput make long read sequencing more economically accessible.