polypolish ☆
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Description:
Short-read polishing tool for long-read assemblies
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics assembly polishing long-read
Install: brew install polypolish
About:
Polypolish is a specialized tool for polishing genome assemblies generated from long-read sequencing data. It works by using paired short-read data to identify and correct insertion, deletion, and substitution errors. Its unique approach focuses on aligning reads to multiple genomic positions, effectively resolving ambiguities and improving assembly accuracy.
Key Features:
  • Error correction for long-read assemblies using short reads
  • Handles multi-mapping reads effectively
  • Designed specifically for diploid genomes
  • Fast and computationally efficient
Use Cases:
  • Polishing assemblies from PacBio or ONT long-read sequencing
  • Improving the accuracy of draft genome assemblies
  • Correcting indels and SNPs in assembled contigs
Alternatives:
  • Pilon – Pilon is a more general-purpose tool, while Polypolish is specifically designed for polishing long-read assemblies with paired short reads.
  • Racon – Racon is typically used for polishing with long reads, whereas Polypolish leverages short reads for correction.
Version History
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