Genomic sequence analysis including genome assembly, sequence alignment, structural variation detection, gene prediction etc. is one of the most classical research areas in bioinformatics and there have been a lot of algorithms and tools for each of these problems. Nevertheless, due to the limitation of sequencing technologies, these problems have not been solved perfectly by existing approaches for a long time. For instance, in genome assembly, problems such as allele-specific genome assembly, tandem repeat assembly, autopolyploid genome assembly and chromosome-level metagenome assembly have not been completely solved. The newest third-generation sequencing technologies like Pacbio Hifi and ONT Ultra-long and genome-wide mapping technologies like Hi-C and Bionano provide opportunities for improving the assemblies of complex genomes in contiguity, correctness and completeness, and for solving other problems in genomic sequence analysis.
Until now, there have been some new approaches and algorithms developed for taking advantage of the newest sequencing data and genome-wide maps to solve the problems left in sequence analysis. For example, in genome assembly, Hifiasm, HiFlye and HiCanu were created for contig assembly with Pacbio Hifi sequences, and ALLHiC, OMGS, Chimericognizer and Novo&Stitch were developed to use Hi-C or BioNano maps to solve the steps of scaffolding, chimeric contig removal or reconciliation in genome assembly. In this Research Topic, we would like to publish two types of works in the area of genomic sequence analysis: (1) the works that applied these methods and tools to achieve important biological findings in plant genomics; (2) the works about creating new approaches and algorithms in this area.
• New approaches and algorithms in genome assembly
• New approaches and algorithms for solving other computational problems in genomic sequence analysis
• Important biological findings achieved by applying existing methods in genome assembly and sequence analysis
Genomic sequence analysis including genome assembly, sequence alignment, structural variation detection, gene prediction etc. is one of the most classical research areas in bioinformatics and there have been a lot of algorithms and tools for each of these problems. Nevertheless, due to the limitation of sequencing technologies, these problems have not been solved perfectly by existing approaches for a long time. For instance, in genome assembly, problems such as allele-specific genome assembly, tandem repeat assembly, autopolyploid genome assembly and chromosome-level metagenome assembly have not been completely solved. The newest third-generation sequencing technologies like Pacbio Hifi and ONT Ultra-long and genome-wide mapping technologies like Hi-C and Bionano provide opportunities for improving the assemblies of complex genomes in contiguity, correctness and completeness, and for solving other problems in genomic sequence analysis.
Until now, there have been some new approaches and algorithms developed for taking advantage of the newest sequencing data and genome-wide maps to solve the problems left in sequence analysis. For example, in genome assembly, Hifiasm, HiFlye and HiCanu were created for contig assembly with Pacbio Hifi sequences, and ALLHiC, OMGS, Chimericognizer and Novo&Stitch were developed to use Hi-C or BioNano maps to solve the steps of scaffolding, chimeric contig removal or reconciliation in genome assembly. In this Research Topic, we would like to publish two types of works in the area of genomic sequence analysis: (1) the works that applied these methods and tools to achieve important biological findings in plant genomics; (2) the works about creating new approaches and algorithms in this area.
• New approaches and algorithms in genome assembly
• New approaches and algorithms for solving other computational problems in genomic sequence analysis
• Important biological findings achieved by applying existing methods in genome assembly and sequence analysis
