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EMBL-PKU / BASALT

MIT License
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Incorporating previous binning attempts #10

Open hrwaik opened 4 months ago

hrwaik commented 4 months ago

Hello,

I was wondering if it was possible to include previous binning results into BASALT at the refinement stage? I have multiple previous outputs from other binners not included in BASALT and would like to combine these with the results of BASALT's autobinner stage.

Thanks Huw

EMBL-PKU commented 3 months ago

Yes. BASALT has a way to feed previous binning bins into it. And then you could the refinement module. To do this, you need to manually use the script "Data_fedding_02282021.py" to feed the data to BASALT. And then, you may use the S5_outlier_remover_DL script to carry out the refinement process. Could you please send me an email to yuke.sz@pku.edu.cn? I will prepare a detailed instruction for doing this. I think I could make an automatic pipeline to accomplish this goal.

EMBL-PKU commented 3 months ago

Sorry for the late response :(

camillaln commented 1 month ago

Hi - I am also interested in doing this. I have two sets of MAGs produced by BASALT that I want to compare to a previous binning dataset. (I could not run all assemblies together due to memory issues ...) Camilla