Polypolish: Short-read polishing of long-read bacterial genome assemblies
Ryan R Wick1, Kathryn E Holt1,2
1Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.
Abstract:
Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. Polypolish performed well in benchmarking tests using both simulated and real reads, and it almost never introduced errors during polishing. The best results were achieved by using Polypolish in combination with other short-read polishers.
Insights
Polypolish improves bacterial genome assembly by fixing errors in repeat regions that are missed by other tools. This new method uses all-per-read alignments for accurate error correction, enhancing genome quality.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Long-read genome assemblies often have errors, particularly in homopolymer regions.
- Existing short-read polishing tools struggle with repeat regions, leaving errors uncorrected.
Purpose of the Study:
- To introduce Polypolish, a novel short-read polishing tool designed to address errors in repeat sequences.
- To evaluate Polypolish's effectiveness in improving bacterial genome assembly accuracy.
Main Methods:
- Development of Polypolish utilizing all-per-read alignments for error correction.
- Benchmarking Polypolish against other polishing tools using simulated and real sequencing data.
Main Results:
- Polypolish successfully repaired errors in repeat regions that were intractable for other polishers.
- The tool demonstrated high accuracy, introducing minimal new errors during the polishing process.
- Combining Polypolish with other short-read polishers yielded the best overall assembly results.
Conclusions:
- Polypolish offers a significant advancement in correcting errors within challenging repeat regions of bacterial genomes.
- The tool enhances the accuracy of long-read-only genome assemblies, particularly when used synergistically with existing methods.
