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Once a Good Assembly Goes Bad, It's Gone Forever

At Omics! Omics!, Keith Robison asks why genomes may not fully assemble. Taking the example of the platypus genome, Robison walks through three possible reasons why assemblies "go bad." First, the platypus genome is chock-full of repeated sequences which can affect assembly. Next, Robison says that either random or non-random under-sampling may have occurred — non-random under-sampling may be due to regions that don't do well growing up in E. coli or that don't PCR up well. Finally, Robison says "assembly rot" could be due to different mutations being introduced into certain regions of the clones while propagating in E. coli.