Nanopolish help please

Hi there,

Does anyone know the paths to call the and scripts that should be part of the nanopolish linuxbrew package?



Their exact location will depend on the version on nanopolish that you have installed, but you should be able to locate the scripts with find:

find /home/linuxbrew -name ""
find /home/linuxbrew -name ""

then run them as suggested in the readme with:

python /home/linuxbrew/.linuxbrew/Cellar/nanopolish/VERSION/scripts/ draft.fa | \
parallel --results nanopolish.results -P 8 nanopolish variants --consensus polished.{1}.fa -w {1} -r reads.fa -b reads.sorted.bam -g draft.fa -t 4 --min-candidate-frequency 0.1

Hi therem,

Thanks for your help.

BTW, I think there is a problem with the latest (0.9.0) linuxbrew package.



Could you elaborate on the problems you’re having with nanopolish?

Yes of course - sorry that wasn’t helpful.

When I tried to run it I’d get “error in nanopolish (fast stop)****” pop up constantly.

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