Due to the constraint of sample, I cannot re-collect the leaves from a genotype that was used for NGS analysis (can only produce draft genome) before. To improve that assembly, can I use the NGS data generated from another genotype (same species but apparently have high heterozygous rate compared to the old one)? If so, please advise for appropriate tool/pipeline and papers dealing with the same issue.
With my appreciation.
Merry K P
Genome complexity: The genome complexity and size can vary significantly among different genotypes, which can affect the quality and completeness of the genome assembly. It is important to ensure that the combined datasets cover the entire genome and do not introduce bias or gaps in the assembly. Differences in sequence quality: The sequence quality and read length can vary among different datasets, which can affect the accuracy and resolution of the assembly. It is important to carefully evaluate the quality of each dataset and perform quality control measures to minimize errors and artifacts. Polymorphisms and variations: Different genotypes can have variations, such as SNPs, indels, and structural variants, that can cause challenges in the assembly process. These variations can create complexities in the assembly, such as chimeric contigs, and can also result in incorrect or incomplete assemblies. Special consideration should be given to these variations, and bioinformatic tools such as haplotype phasing and polishing should be used to resolve them. Computing resources: Combining sequence datasets from different genotypes can increase the computational requirements, especially for large and complex genomes. Sufficient computational resources, such as high-performance computing clusters, are required to process and analyze the datasets efficiently.
Combining sequence datasets from different genotypes can potentially improve genome assembly quality, especially for regions that are highly variable or difficult to sequence. However, there are several challenges that need to be considered when combining sequence datasets from different genotypes:
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