Add DESMAN to STRONG - Githubissues

chrisquince / STRONG

Strain Resolution ON Graphs

MIT License

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Add DESMAN to STRONG #16

Closed chrisquince closed 5 years ago

chrisquince commented 5 years ago

Add DESMAN to STRONG pipeline as additional snake that is called with a flag from the start.py script. An example DESMAN tutorial is here:

https://github.com/chrisquince/Ebame4/blob/master/StrainResolution.md

Sebastien-Raguideau commented 5 years ago

Snakemake is working for up to Desman execution. For now I am not using Sergey proposed pipeline, issue with a hard coded parameter on number of SNV=3000. Also maybe not critical but there is no error prior which can be passed to desman. TO DO :

select the max number of strains automatically
integrate Desman as a possible output with some flags.

Sebastien-Raguideau commented 5 years ago

Can't seem to make resolvenhap.py works, would be useful for setting the max nb of strains. Current Desman snake stop after outputing the Deviance plot.

chrisquince commented 5 years ago

OK when I come in (~3pm) we can have a go at getting this to work.