9/02/14
Customer asks for constructing a computational pipeline to discriminate several strains of the same bacterial species; the reference genome of the species is available. AccuraScience LB initially discusses the routine SNV/Indel calling pipeline, followed by comparison of SNVs/Indels identified across the strains. Customer says the purposes of the work is to develop PCR targets able to discriminate between the strains. It is expected that horizontal gene transfer events have frequently taken place which set the strains apart. AccuraScience LB and Customer talk on the phone about the specific requirements, following which AccuraScience LB sends a revised pipeline.
Wed, 09/03/2014 at 1:36 PM
AccuraScience LB: As we discussed, the SNP and Indel calling pipeline referred to in a previous round of email communication would not be adequate for your purposes. The approach we would take to obtain differences between strains/serial types, for purposes of identifying proper regions to design PCR primers against, would include the following steps: (1) map all reads to the reference genome, (2) perform a de novo assembly for the unmapped reads, the result of which will be a number of sequence stretches (called contigs), (3) optionally, do a blast search using the contigs against all known bacterial sequences, to attempt to functionally annotate them, and (4) compare the contigs across the strains and produce a list of unique contigs for each strain.
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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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