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Deciding Factors

In a post from the [mira_talk] mailing list on Free Lists, Bastien Chevreux shares tips for beginning a sequencing project. "Please bear with me if I look at sequencing a bit differently than you might be accustomed to from academia, but I have worked for quite some time now in industry, and there cost-effectiveness, respectively 'probability of success' of a project as whole, is paramount to everything else," Chevreux begins. He breaks a hypothetical sequencing project into its parts — sample prep, data generation, assembly, and annotation — saying that "depending on what you are really interested in within your project and what you expect to be able to do with the sequencing data, one can cut corners and reduce cost here and there (but not everywhere)."

Some researchers can't afford do their sequencing in-house, or find that doing so is not cost-effective. When it comes to choosing a sequencing service provider, Chevreux suggests considering "'Whom do I trust to deliver good work?' Intuition says that institutes with a long sequencing history have amassed quite some knowledge in this field, making them experts ... and intuition probably isn't wrong there," he says. "The same thing is probably true for sequencing companies which have existed for more than just a couple of years." He notes, though, that some sequencing companies sometimes focus on data generation rather than assembly and annotation.

Overall, Chevreux says, it's important to center all sequencing project-related decisions on the desired outcome. "Every other question — like where to sequence, which sequencing technology to use, how to process the sequencing data afterwards — is incidental and subordinated to your answer to the question of 'What do you want?'" he says.

HT: Keith Bradnam

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