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Team Seven Bridges – Telelink Case: What Really Goes into Sausages?

The food industry is governed by strict laws and regulations, which provide certainty that each product meets health and safety standards. In addition to existing biochemical food product analysis, we propose a metagenomic approach. Main benefit of this approach is the ability to perform next generation sequencing as a standard first step and then align the sampled data to genomes references of many organisms suspected to be present in the sample. Additionaly, if another organism is suspected at a later date, it is easy to reause the sampled data set to perform another analysis – in the biochemical analysis this would require expensive sample storage and performing more laboratory tests. We examined three approaches to metagenomic analysis – BLAST, Centrifuge and BWA MEM.

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9 thoughts on “Team Seven Bridges – Telelink Case: What Really Goes into Sausages?

  1. 2
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    Great article! and I can see you’re still altering and adding sections to it. It seems you have dedicated a lot of attention to the tools used to create the model. It would be great to also write about problems you encountered and how you have solved them, as well as open questions/problems that still should be solved.

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      Thanks! We were in a time scramble at the end. This challenge is very interesting, and we think more time should be dedicated to shaping the final solution.

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    I really liked this article, because they went beyond the given setting and actually suggest that there are potentially other organisms in there, too. Interested whether the Taenia and Rat are true hits and if these few fragments are enough evidence for potential contamination. Great research skills!

  3. 1
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    Congratulations! You have done an amazing job! The results are excellent! Also, you revealed the secret in the 1001th read. I think you deserve the victory.

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    Questions during the presentation:
    1. @drceenish
    Can this approach become a real product in the world which one day we can walk with in the supermarket? Your thoughts?
    2. @liad
    – How would you tackle gene mutations or unknown samples which were not in the gene bank? or (even worse) if the sample in the bank are not accurate

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      For each index it took ~1-2hours, while alignment of the sample data to each reference genome took <30min.

      In the attached BWA jupyter notebook, in #data understanding cell you can see the following list comprehension:

      weird = [elem for elem in seqs if elem not in seqb]

      it lists all the elements in the "small" sample (seqs) which are not present in the "big" sample (seqb).

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