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marbl / Winnowmap

Long read / genome alignment software
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Winnowmappy #7

Open marcus1487 opened 3 years ago

marcus1487 commented 3 years ago

This project looks very promising. Is it possible/are there plans to provided a python interface (winnowmappy) to this software?

For some more detail, I am the developer of the Oxford Nanopore Technologies Megalodon software. I would be interested in seeing how this mapping could improve results in repeat regions. Within Megalodon, I currently use the mappy python interface to minimap2. I am wondering if it might be possible to port the mappy interface into this project? I'm not sure how diverged this project is from minimap2 to make this possible, but this would be very helpful to assist future research.

cjain7 commented 3 years ago

Hi @marcus1487

I'm happy to investigate this. But I wonder if it would be a worthwhile exercise at your end to verify whether Winnowmap is giving you desirable improvements first (?) I'd assume there are ugly work-arounds to call C++ binary from python code. Let me know what you think.