Polypolish

Polypolish polishes genome assemblies using short-read all-per-read alignments from SAM files to correct assembly errors, particularly in repeat regions and homopolymer-length inaccuracies.

Key Features:

• All-per-read alignments (SAM): Uses all-per-read alignments from SAM files so each read can align to multiple potential locations rather than only a single best alignment.
• Repeat-region error correction: Targets and repairs errors in repeat regions that are often resistant to conventional alignment-based polishers.
• Homopolymer-length correction: Addresses homopolymer-length inaccuracies commonly found in long-read-only assemblies.
• Short-read polishing for long-read assemblies: Applies short-read data to refine long-read-only bacterial genome assemblies.
• Benchmark-validated accuracy: Demonstrated in benchmarking with simulated and real reads to repair errors without introducing new ones.
• Complementary polishing: Can be used in combination with other short-read polishers to achieve improved assembly accuracy.

Scientific Applications:

• Refinement of bacterial assemblies: Polishes long-read-only bacterial genome assemblies using short-read data to reduce residual errors.
• Repeat and homopolymer correction: Improves base-level accuracy in regions with repeats and homopolymer-length errors.
• Benchmarking and method comparison: Serves in evaluations using simulated and real reads to assess polishing performance and error introduction.

Methodology:

Polypolish uses all-per-read alignments from SAM files, allowing each read to be aligned to multiple potential locations rather than being restricted to a single best alignment.