minipolish

minipolish polishes genome assemblies generated from Oxford Nanopore Technologies and Pacific Biosciences long reads to correct sequencing errors, support contig circularization, and provide read-depth information for prokaryotic genomes.

Key Features:

• Integration with Miniasm and Racon: Bridges Miniasm assembly output to Racon for iterative polishing of draft assemblies.
• Sequencing error correction: Corrects long-read sequencing errors to improve contig accuracy.
• Read depth reporting: Provides read depth information per contig to assess coverage and identify regions of interest.
• Contig circularization support: Produces clean contig circularization relevant for plasmid and chromosome assemblies.

Scientific Applications:

• Prokaryotic genome assembly polishing: Improves accuracy of bacterial and archaeal genome assemblies derived from long reads.
• Downstream genomic analyses: Enables more reliable gene annotation, comparative genomics, and evolutionary studies by reducing assembly errors.

Methodology:

Bridges Miniasm output to Racon for polishing and was evaluated using 500 simulated read sets and 120 real read sets across genomes and parameters to assess contig circularization and read-depth metrics.