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rvalieris / LCS

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Spped up the process : prepration of markers file. #15

Open vinayrajput0005 opened 1 year ago

vinayrajput0005 commented 1 year ago

Hi, Can we speed up the pipeline ?!! If I want to add some new lineage to variants table, the tools is taking 2 days to complete it. Is there any way to do it faster, by adding more threads.!!

rvalieris commented 1 year ago

hello, can you give me more details - are you using gisaid or ucsc sequences ? and what does your variant groups looks like ?

to speed things up I recommend using the ucsc method of creating the markers file, also consider downsampling the sequences like I suggested here: https://github.com/rvalieris/LCS/issues/6#issuecomment-1115327306