Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

November 2012 | Volume 7 | Issue 11 | e47768 | Adam C. English*, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M. Muzny, Jeffrey G. Reid, Kim C. Worley, Richard A. Gibbs
The article "Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology" by Adam C. English et al. presents an automated approach to finishing draft genomes using long-read sequencing data from the Pacific Biosciences RS (PacBio) platform. The authors developed PBelly, a software tool that aligns long reads to draft assemblies to close or improve gaps. The tool is designed to be fast, accurate, and reproducible, and it preserves existing annotations. The study demonstrates the effectiveness of PBelly by applying it to four draft genome assemblies: a simulated *Drosophila melanogaster*, the version 2 draft *Drosophila pseudoobscura*, an Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, the method addressed 99% of gaps in *D. pseudoobscura* and closed 69% of gaps, improving 12%. Similar improvements were observed in other datasets. The accuracy of gap closure was validated by comparing PBelly-generated sequences with Sanger sequencing data, showing a mean percent similarity of 91.7%. The authors also discuss the limitations and future improvements of the method, including the need for higher-quality long-read technologies and better scaffolding software.The article "Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology" by Adam C. English et al. presents an automated approach to finishing draft genomes using long-read sequencing data from the Pacific Biosciences RS (PacBio) platform. The authors developed PBelly, a software tool that aligns long reads to draft assemblies to close or improve gaps. The tool is designed to be fast, accurate, and reproducible, and it preserves existing annotations. The study demonstrates the effectiveness of PBelly by applying it to four draft genome assemblies: a simulated *Drosophila melanogaster*, the version 2 draft *Drosophila pseudoobscura*, an Assemblathon 2.0 budgerigar dataset, and a preliminary assembly of the Sooty mangabey. With 24× mapped coverage of PacBio long-reads, the method addressed 99% of gaps in *D. pseudoobscura* and closed 69% of gaps, improving 12%. Similar improvements were observed in other datasets. The accuracy of gap closure was validated by comparing PBelly-generated sequences with Sanger sequencing data, showing a mean percent similarity of 91.7%. The authors also discuss the limitations and future improvements of the method, including the need for higher-quality long-read technologies and better scaffolding software.
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