The study presents an automated method for upgrading draft genomes using long-read sequencing technology from the Pacific Biosciences RS (PacBio) platform. This approach, called PBJelly, uses long reads to close gaps and improve the quality of draft genome assemblies. The method involves aligning long reads to a reference genome, identifying gap-supporting reads, and assembling these reads to generate high-quality consensus sequences. PBJelly also generates "lift-over" tables to transfer annotations to the upgraded assembly. The study tested PBJelly on four datasets: a simulated Drosophila melanogaster genome, the version 2 draft of Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the sooty mangabey. With 24× mapped coverage of PacBio long-reads, PBJelly closed 69% of gaps and improved 12% of gaps in D. pseudoobscura. With 4× mapped coverage, it closed 32% of gaps and improved 63% in the budgerigar assembly. With 6.8× mapped coverage, it closed 66% of gaps and improved 19% in the sooty mangabey assembly. The accuracy of gap closure was validated by comparing the results with Sanger sequencing. The study found that the accuracy of gap closure was dependent on the initial reference quality. PBJelly was able to significantly reduce the number of gaps and improve the quality of the assemblies. The method is efficient, scalable, and can be applied to various genome assemblies. The study also discusses the limitations of the method, including the inability to close all gaps and the presence of overfilled gaps. However, the overall results demonstrate the effectiveness of using long-read sequencing technology to upgrade draft genomes. The study concludes that PBJelly provides a powerful tool for improving genome assemblies and is a valuable resource for the genomics community.The study presents an automated method for upgrading draft genomes using long-read sequencing technology from the Pacific Biosciences RS (PacBio) platform. This approach, called PBJelly, uses long reads to close gaps and improve the quality of draft genome assemblies. The method involves aligning long reads to a reference genome, identifying gap-supporting reads, and assembling these reads to generate high-quality consensus sequences. PBJelly also generates "lift-over" tables to transfer annotations to the upgraded assembly. The study tested PBJelly on four datasets: a simulated Drosophila melanogaster genome, the version 2 draft of Drosophila pseudoobscura, an assembly of the Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the sooty mangabey. With 24× mapped coverage of PacBio long-reads, PBJelly closed 69% of gaps and improved 12% of gaps in D. pseudoobscura. With 4× mapped coverage, it closed 32% of gaps and improved 63% in the budgerigar assembly. With 6.8× mapped coverage, it closed 66% of gaps and improved 19% in the sooty mangabey assembly. The accuracy of gap closure was validated by comparing the results with Sanger sequencing. The study found that the accuracy of gap closure was dependent on the initial reference quality. PBJelly was able to significantly reduce the number of gaps and improve the quality of the assemblies. The method is efficient, scalable, and can be applied to various genome assemblies. The study also discusses the limitations of the method, including the inability to close all gaps and the presence of overfilled gaps. However, the overall results demonstrate the effectiveness of using long-read sequencing technology to upgrade draft genomes. The study concludes that PBJelly provides a powerful tool for improving genome assemblies and is a valuable resource for the genomics community.