What are the advantages of different sequencing platforms in de novo sequencing of animal and plant genomes?
The second generation sequencing platform, represented by Illumina, has the advantages of large amount of sequencing data and low cost, and can provide high coverage data for genome sequencing. However, the platform has the characteristics of reading length and GC preference, so it is difficult to cross the repeat sequence region and high GC content region. The third generation sequencing platform, represented by PacBio RS II and sequel platforms, has the advantages of long reads (average reads length > 10 KB), fast sequencing (short running time, single SMRT cell running time is 2-6 hours), high throughput (average each SMRT cell generates ~ 8G of effective data), no GC preference, detection of base modification information (including methylation modification), and no PCR bias (do not need PCR amplification, avoid the heterogeneity of sequencing coverage) and other characteristics, especially suitable for the de novo sequencing of animal and plant genomes. According to the characteristics and complexity of the genome of species, Personalbio will scientifically design the sequencing experiment scheme, and reasonably use multiple platforms together, which can not only solve the sequencing problem of complex genome, ensure the quality of genome sequencing, but also take into account the budget of the experiment project.
Why do different types of libraries need to be built for animal/plant genome de novo sequencing projects?
Because animal and plant genomes are large and complex, and there are a large number of repeat regions, it is necessary to prepare sequencing libraries with different gradients, and carry out double terminal sequencing, so that large-scale repeat regions can be skipped in assembly and improve the quality of assembly. At the same time, combined with the BAC or Fosmid library and the comprehensive application of a variety of sequencing platforms, it ensures the accuracy of sequencing and the integrity of the genome, and efficiently and economically completes the genome mapping of higher animals and plants.
What is the difference between a genome framework map and a fine map?
The frame map can cover 90% of the autosomal region, 95% of the gene region, contig N50 to 5 KB, scaffold N50 to 20 KB, and the single base error rate is less than 1 / 100000. The fine map can cover 95% of the autosomal region, 98% of the gene region, contig N50 to 20 KB, scaffold N50 to 300 KB, and the single base error rate is less than 1 / 100000.
