Comments (5)
I agree with the comment of @betteridiot above. I also think this is the biggest weakness of the recan
. While the package offers a very good visualisation tool for analysing genetic similarity, I would not call it a recombination detection tool since the detection requires completely manual assessment of the similarity plots.
In modern contexts, where we often have to work with a lot of data at once, I think it would be extremely helpful if recan
can incorporate a method to detect potential recombination events.
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I'm going to add a function which will go through the alignment and predict recombination break points based on genetic distance change. However, I need to collect and analyze more information on the confirmed recombination cases to set reasonable distance change parameters that seem to be different for RNA and DNA viruses.
Maybe it'll be better now to rename the paper to "Recan: Python tool for analysis of recombination events in viral genomes", as the package has no this function.
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I'd like to proceed the review process with renaming the article to "Recan: Python tool for analysis of recombination events in viral genomes".
https://github.com/babinyurii/recan/blob/master/paper/paper.md
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I understand that developing a method for recombination detection is not easy and will take some time. Perhaps, you may want to consider incorporating a currently existing method into your package.
For the moment, I think changing the title of the paper is good enough.
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I agree with @lamhm
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Related Issues (15)
- JoSS Review: Community Guidelines HOT 1
- JoSS Review: Installation HOT 1
- JoSS Review: README Documentation HOT 1
- JoSS Review: Example Usage HOT 5
- JoSS Review: Automated tests HOT 2
- Distance Calculation HOT 2
- JoSS Review: Statement of need HOT 2
- JoSS Review: Quality of writing HOT 4
- JoSS Review: Performance HOT 2
- ValueError: Sequences must all be the same length
- Copyright statement HOT 1
- save_data: TypeError: 'NoneType' object is not subscriptable HOT 2
- k2p: ZeroDivisionError: float division by zero HOT 2
- recan R package
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