JASPER

JASPER polishes genome assemblies derived from long-read sequencing technologies (e.g., nanopore) by correcting consensus errors using Jellyfish-derived k-mer counts without aligning reads to the assembly.

Key Features:

• K-mer Based Polishing: Uses a database of k-mer counts derived from sequencing reads (generated with Jellyfish) to detect and correct consensus errors.
• Efficiency: Avoids read-to-assembly alignment by operating on k-mer counts, reducing computational mapping overhead.
• Accuracy: Experimental comparisons demonstrated higher accuracy than other k-mer-based polishing methods.
• Population-Specific Reference Generation: Can be applied to polish assemblies from multiple individuals to produce population-specific reference genomes that better represent population variation.

Scientific Applications:

• De Novo Genome Assemblies: Improves consensus accuracy of de novo assemblies from long-read data to support downstream analyses.
• Population Genomics: Enables creation of population-specific reference genomes by polishing assemblies from multiple individuals to aid studies of genetic diversity and population-specific variants.
• Clinical Genomics: Enhances assembly accuracy in clinical genomics workflows where precise consensus sequences are required for variant discovery.

Methodology:

Builds a database of k-mer counts from sequencing reads using Jellyfish and compares assembly k-mers to the read-derived counts to identify and correct consensus errors, operating without aligning reads to the assembly.