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gaolabtools / scNanoGPS

Single cell Nanopore sequencing data for Genotype and Phenotype
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Running time of scNanoGPS v1.1 assigner.py #9

Closed shiauck closed 1 year ago

shiauck commented 1 year ago 
Hi Cheng-Kai,
Thank you for updating scNanoGPS!
I used scNanoGPS-1.1 and found that it is much faster in assigner.py compared to scNanoGPS-1.0. It may have taken a week before, but now it only takes nearly 2 hours. Is this normal?
![image](https://github.com/gaolabtools/scNanoGPS/assets/87375686/e2bcd29b-8f78-4285-beca-05d835dfc166)
Here is my code:
`python $scNanoGPS_dir/assigner.py -i $Output_dir/barcode_list.tsv.gz -d $Output_dir -t 35`
I don't think the new parameters will have any issues with my original code.

Thank you for your reply!
Best wishes,
Kirito

Originally posted by @kir1to455 in https://github.com/gaolabtools/scNanoGPS/issues/8#issuecomment-1704916962

shiauck commented 1 year ago

Hi Kirito,

Thanks for trying the new version. Yes, I updated assigner.py in scNanoGPS v1.1 and it is much much more efficient than before. In our sample (~100M reads, <10K cell barcodes), it takes around 6 hours to finish assigner step with 20 cores.

I also added some new parameters in scNanoGPS v1.1. Please check the Github README.

Thank you so much. I really appreciate your feedback.

Regards, Cheng-Kai