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Hybrid genome assembly
In bioinformatics, hybrid genome assembly refers to utilizing various sequencing technologies to achieve the task of assembling a genome from fragmented, sequenced DNA resulting from shotgun sequencing. Genome assembly presents one of the most challenging tasks in genome sequencing as most modern DNA sequencing technologies can only produce reads that are, on average, 25-300 base pairs in length.〔Pop, M. (2009). Genome assembly reborn: recent computational challenges. Brief Bioinform, 10(4), 354-366. doi: 10.1093/bib/bbp026.〕 This is magnitudes smaller than the average size of a genome (the genome of the octoploid plant ''Paris japonica'' is 149 billion base pairs 〔Pellicer, Jaume, Fay, Michael F., & Leitch, Ilia J. (2010). The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society, 164(1), 10-15. doi: 10.1111/j.1095-8339.2010.01072.x〕). This assembly is computationally difficult and has some inherent challenges, one of these challenges being that genomes often contain complex tandem repeats of sequences that can be thousands of base pairs in length.〔Alkan, C., Sajjadian, S., & Eichler, E. (2011). Limitations of next-generation genome sequence assembly. Nature Methods, 8.〕 These repeats can be long enough that second generation sequencing reads are not long enough to bridge the repeat, and, as such, determining the location of each repeat in the genome can be difficult.〔Koren, S., Harhay, G., Smith, P., Bono, J., Harhay, D., Mcvey, S., . . . Phillippy, A. (2013). Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology.〕 Resolving these tandem repeats can be accomplished by utilizing long third generation sequencing reads, such as those obtained using the PacBio RS DNA sequencer. These sequences are, on average, 10,000-15,000 base pairs in length and are long enough to span most repeated regions.〔http://blog.pacificbiosciences.com/2014/10/new-chemistry-boosts-average-read.html〕 Using a hybrid approach to this process can increase the fidelity of assembling tandem repeats by being able to accurately place them along a linear scaffold and make the process more computationally efficient.
==Genome Assembly==
抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』
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