Comments (4)
sjanssen2
commented on July 17, 2024
Can we simulate distance matrices where we know the best prototypes?
Low noise background for total matrix + high noise for prototypes?!
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sjanssen2
commented on July 17, 2024
@wasade any idea if skbio distance matrix objects are able to load a 1m x 1m matrix into memory?
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qiyunzhu
commented on July 17, 2024
@sjanssen2 If the prototypes mean genomes, I believe we can. Just do MinHash. But maybe you meant something else?
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sjanssen2
commented on July 17, 2024
I think this issue has been addressed. Benchmarking notebook is now in.
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Related Issues (10)
- write Readme.md
- move prototype selection code from WGS-HGT HOT 2
- adding seedsets to other prototype functions
- to add a parser of RepoPhlAn output
- to implement code for calculating genome quality scores
- to add wrappers for Mash, pyani, phyletic pattern-based tools for computing genome pairwise distances
- to implement a biological popularity ranking system based on PubMed hits count
- to design and implement a benchmarking system HOT 1
- Conda recipes
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