Structured PREreview of INAEME: Integral Neoantigen Analysis with Entirety of Mutational Events

Does the introduction explain the objective of the research presented in the preprint?

Partly

Early in the abstract, the authors talk about neoantigens are and they move on to neoantigen discovery. If they can include what is neoantigen discovery, how it is useful, then the information flow will be much more natural. I do see a much detailed and beautiful explanation of the background in the introduction. However, after describing some of the other tools that exist out there, the authors do not mention in detail what they attempted and how in the introduction.

Are the methods well-suited for this research?

Somewhat appropriate

The precision and recall curves seem noisy. The knee portions of the curves do not have sufficient data.

Are the conclusions supported by the data?

Highly supported

Are the data presentations, including visualizations, well-suited to represent the data?

Somewhat appropriate and clear

I applaud the authors' work in trying to get the truth datasaet through the TESLA challenge. A confusion matrix to present the results would probably be more appropriate here.

How clearly do the authors discuss, explain, and interpret their findings and potential next steps for the research?

Somewhat clearly

The entire paper has been written well with clear and concise explanation. However, it would be useful to see what the authors think the weakness in their tool is and what the next steps would be.

Is the preprint likely to advance academic knowledge?

Highly likely

Would it benefit from language editing?

No

There are a few typos and in couple of places consecutive commas in between words. However, it does not hinder the understanding of the paper.

Would you recommend this preprint to others?

Yes, it’s of high quality

Is it ready for attention from an editor, publisher or broader audience?

Yes, after minor changes

1. Just a few grammatical minor errors. 2. A confusion matrix when challenged against truth dataset. 3. A small blurb on what is missing in the algorithm currently and what the next steps would be.

Competing interests

The author declares that they have no competing interests.