The necessity of clair3 and medaka in conda enviroment

[awesomedeer]

Dear Fan,@lemene
Thanks for developing this nice assembly software! I was wondering if it will influence the results without clair3 and medaka since I met some issues when I try to install them in conda. I mean basically that with these two we will have better results? Or if these two have conflicts, which one we should keep in conda enviroment?

Best regards
Song

[lemene]

@awesomedeer
Unfortunately, clair3 and medaka conflict within the conda environment. see https://github.com/lemene/PECAT?tab=readme-ov-file#installing-and-configuring-clair3-and-medaka. Here are some solutions. Do not install clair3 and medaka directly; instead, use Docker or Singularity to invoke them.

[awesomedeer]

Thanks for the fast and detailed response! So it means probably that I can't use theses two if I don't have the admin account/permission since these docker&singularity need.

[lemene]

Hi @awesomedeer
Without Clair3, tool performance in low heterozygosity regions may be affected. Medaka can improve the base accuracy of assemblies. But they are not necessary. A cumbersome solution is to install Clair3 first, and then install Medaka during the polishing step.

[awesomedeer]

Thanks for the answer! I will try this solution and will update here if it will work and be helpful other people.