09/18/14
Thu, 09/18/014 at 8:06 AM
Customer: Do you have any experience with bacterial genomes? Especially those genomes that have both chromosomal and plasmid DNA. De nove assembly of the plasmids seems to give many bioinformatics people a very tough time.
Thu, 09/18/2014 at 8:56 AM
AccuraScience LB: Current computational pipelines work reasonably well for assembling reads into contigs for bacterial genome projects. When there are a dozen or a couple of dozen larger contigs remaining, it is important to not just trust the results produced by the computational methods, but rather, examine and rearrange them manually - in order to achieve the optimal assembly. This would be a time consuming and expensive effort, but if you are really critical about the quality of the assembly, this would be necessary.
If this manual examination is conducted, then a genome with both chromosomal and plasmid DNA is not necessarily more challenging than one with only a chromosome.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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