![]() ![]() ![]() Besides PacBio, other long-read sequencing platforms such as Oxford Nanopore are being used to assemble genomes at high accuracy 8.Įven with the improvement in long-read sequencing, additional approaches are required to accurately scaffold contigs. Fortunately, PacBio sequencing errors appear randomly distributed, therefore, with sufficient depth, a consensus with high per base sequence quality can be achieved. However, the relatively low throughput and higher error rates (~11–15%) remain a problem. This has facilitated the high quality assembly of mammalian genomes, including the gorilla 6 and the goat 7. The latest PacBio single-molecule sequencing technologies 4 deliver mean read lengths above 10 kb, with reads as long as 60 kb 5. Fully assembling a mammalian genome is still challenging, and even the current human genome assembly (GRCh38), that has received considerable input of money and resources from more than 10 institutions and over 1000 researchers, still contains hundreds of gaps 3. Therefore, additional data types are required to correctly order and orient contigs. Mammalian genomes contain large families of repeats that are difficult to span, even with longer sequence reads, which, together with insufficient sequence coverage, result in breaks in sequence contiguity. For smaller haploid genomes, such as bacteria, complete assembly is now possible at relatively low cost 2 but the same does not apply to larger complex diploid or polyploid genomes. However, despite advances in sequencing technologies, our ability to generate long contiguous DNA sequence reads is still limited, necessitating the use of a number of assembly algorithms and technologies to piece together the genomic jigsaw. A finished, accurate haplotype-resolved reference genome is necessary to understand the biology of a species, manage genetic diversity and, in the case of livestock, to apply genomic selection for genetic improvement 1.
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