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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Puzzler: scalable one-command platinum-quality genome assembly from HiFi and Hi-C
Justin Merondun1,2, Qingyi Yu1
1Tropical Plant Genetic Resources and Disease Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Hilo, HI 96720, United States.
Bioinformatics Advances
|January 23, 2026
Summary
Puzzler is a new pipeline for creating high-quality chromosome-scale genome assemblies using HiFi and Hi-C data. This user-friendly tool automates complex bioinformatic processes, enabling faster and more efficient genomic research.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Chromosome-level genome assemblies are crucial for various genomic applications, including comparative genomics, evolutionary studies, and precision breeding.
- Current bioinformatic pipelines for high-quality genome assembly using HiFi and Hi-C data are complex, requiring specialized expertise and tools.
- The increasing demand for large-scale pan-genomic projects necessitates scalable, portable, and user-friendly assembly solutions.
Purpose of the Study:
- To introduce Puzzler, a containerized and scalable pipeline designed for automated chromosome-scale *de novo* genome assembly.
- To streamline and standardize high-quality genome assembly workflows, reducing complexity and user input.
- To enable high-throughput generation of platinum-quality genomes for large-scale genomic initiatives.
Main Methods:
- Puzzler utilizes PacBio HiFi and Hi-C data for *de novo* genome assembly.
- The pipeline automates contig assembly, duplicate purging, Hi-C-based scaffolding, and chromosome assignment using synteny.
- Integrated quality control includes Hi-C contact maps, BUSCO, yak k-mer completeness, and BlobTools contamination screening.
Main Results:
- Puzzler successfully generated highly contiguous chromosome-scale assemblies across a wide range of genome sizes (24 Mbp to 6.5 Gbp).
- The pipeline requires minimal user input (<10 minutes), demonstrating its user-friendliness and efficiency.
- Automated processes and integrated quality control ensure standardized, high-quality genome assembly outputs.
Conclusions:
- Puzzler provides a scalable, portable, and user-friendly solution for high-throughput chromosome-scale genome assembly.
- The pipeline simplifies complex bioinformatic workflows, making advanced genomics accessible to a broader range of researchers.
- Puzzler facilitates large-scale pan-genomic efforts by standardizing the generation of platinum-quality genomes.
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