1/12/2015
Customer inquires about options of analyzing sequencing data from a large number of virus strains.
Mon, Jan 12, 2015 at 9:11 AM
AccuraScience LB: I looked up the literature, and found that the genome of at least one strain of this viral species has been available, which could possibly be used as a reference. If many large-scale structural changes on chromosomes (e.g., inversions, translocations) are expected to have taken place between the strains you sequence and the existing, reference genome, then de novo assembly might be a good strategy to handle your data. If these structural changes are not expected to have happened, and the difference between your strains and the reference genome is expected to be mostly SNVs (single nucleotide variations), and small Indels (insertions and deletions), then a mapping based strategy (in contrast to de novo assembly) - followed by SNV and Indel calling - would be more proper, because the latter takes full advantage of the available reference genome, and is less error-prone. Therefore, whether we will do de novo assembly, or mapping followed by SNV/Indel calling would have to be your decision, based on your expert knowledge of the strains you work on.
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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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