Third-generation sequencing (TGS), including Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing, and the Oxford Nanopore Technologies (ONT) sequencing platform, works by reading long nucleotide sequences at the single molecule level with high-quality. In contrast to next-generation sequencing that requires breaking long strands of DNA into a few hundred of short reads, then inferring nucleotide sequences by amplification and synthesis, TGS has been proven to be one of the most efficient approaches to determine the genome sequence of a species or an individual in a population. However, the accurate identification of nucleotide bases and high raw read error rates (10% to 30% error) data generated by TGS technologies bring many computational challenges, including filtering and correcting low-quality reads, producing highly accurate de novo assemblies of microbial, plant and animal genomes, more complete and accurate representations of genes, clinically relevant SNPs, regulatory regions, and other important genomic elements, as well as better resolution of the overall chromosome organization, etc.
This Research Topic will focus on the recent progress of bioinformatics methods and applications for third-generation sequencing. We welcome the submission of original research and review articles on the following subjects:
- New algorithm and computational tool developments for third-generation sequencing, such as the novel strategies or improved methods for de novo genome assembly, full-length transcriptome analysis; the algorithms and statistical models for SNP and structural variation (SV) detection, functional annotation, and haplotype phasing, etc; the integrated pipelines and visualization tools for sequencing data from PacBio or ONT sequencing platforms.
- DNA methylation, as it is an important epigenetic modification tool and has attracted a lot of attention. Recently, the developed TGS technology provided an efficient way to detect various types of modification, such as 6mA, 5mC, and 4mC, etc. Due to the lack of detection methods, some new modification types such as 5hmC and 1mA detection are limited. Thus, this subject welcomes the development of the methods for direct measurement of epigenetic modifications from single molecules, methyltransferases to be discovered and for the role of methylation modifications.
- TGS applications, as it contributes to genetics, disease diagnosis, drug discovery, precision medicine, etc. Besides the performance evaluation of existing or novel methods using simulated and experimental data sets, reviews of recent methodological developments about TGS are also welcome.
Third-generation sequencing (TGS), including Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing, and the Oxford Nanopore Technologies (ONT) sequencing platform, works by reading long nucleotide sequences at the single molecule level with high-quality. In contrast to next-generation sequencing that requires breaking long strands of DNA into a few hundred of short reads, then inferring nucleotide sequences by amplification and synthesis, TGS has been proven to be one of the most efficient approaches to determine the genome sequence of a species or an individual in a population. However, the accurate identification of nucleotide bases and high raw read error rates (10% to 30% error) data generated by TGS technologies bring many computational challenges, including filtering and correcting low-quality reads, producing highly accurate de novo assemblies of microbial, plant and animal genomes, more complete and accurate representations of genes, clinically relevant SNPs, regulatory regions, and other important genomic elements, as well as better resolution of the overall chromosome organization, etc.
This Research Topic will focus on the recent progress of bioinformatics methods and applications for third-generation sequencing. We welcome the submission of original research and review articles on the following subjects:
- New algorithm and computational tool developments for third-generation sequencing, such as the novel strategies or improved methods for de novo genome assembly, full-length transcriptome analysis; the algorithms and statistical models for SNP and structural variation (SV) detection, functional annotation, and haplotype phasing, etc; the integrated pipelines and visualization tools for sequencing data from PacBio or ONT sequencing platforms.
- DNA methylation, as it is an important epigenetic modification tool and has attracted a lot of attention. Recently, the developed TGS technology provided an efficient way to detect various types of modification, such as 6mA, 5mC, and 4mC, etc. Due to the lack of detection methods, some new modification types such as 5hmC and 1mA detection are limited. Thus, this subject welcomes the development of the methods for direct measurement of epigenetic modifications from single molecules, methyltransferases to be discovered and for the role of methylation modifications.
- TGS applications, as it contributes to genetics, disease diagnosis, drug discovery, precision medicine, etc. Besides the performance evaluation of existing or novel methods using simulated and experimental data sets, reviews of recent methodological developments about TGS are also welcome.
