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I would like to include Sage (https://github.com/lazear/sage), as it is fast/state-of-the-art. However, we need to make a converter for the output to get it into mzIdentML (I asked the developer, but he wasn't too keen on it...).
We can either look at this list, but we should discuss a set of tools that are not difficult to implement but would allow more diverse workflows.
Each tool should include a workflow example + data to run it.
Feel free to edit the following list to make a final list:
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