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Old 07-21-2019, 09:03 PM   #3
Location: Stony Brook, NY

Join Date: Aug 2013
Posts: 13

Hi tamu_anand,

I think this is an interesting question, and one that I'm not certain has a clearly "right" or "wrong" answer. While peer-review and publication of the paper associated with a method can be important for many reasons, the utility (or correctness or accuracy) of the method is obviously independent of that event. Also, while I can understand why some might use the existence of a "published" paper as a filter for considering the use of a method, I personally consider it neither necessary nor sufficient. GenoMax brings up the prototypical example (but it's a great one) of BWA-mem. Generally, my filter for deciding to use a tool or not is based upon understanding, at some level, what it is doing and also testing it, if reasonable data is available for doing that.

It's also worth pointing out that salmon, like many genomics tools, functions as a platform for research. This means that new ideas and approaches are explored quite frequently, and when they seem useful, they are often exposed to users. The more thoroughly the features are tested, the more prominent they become. Sometimes, as in the case of SA, the tool developers choose to write a manuscript about them. Other times, however, the features may become available but not be accompanied by any manuscript. In such cases, it's my belief in the utility of the feature / improvement and not the publication status of any associated manuscript that primarily determines if I will use it. Otherwise, I might be missing out on useful or important features while waiting for a manuscript that may never come.
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