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cguccione / human_host_filtration

Pipeline which removes human DNA from microbial shotgun samples.
BSD 3-Clause "New" or "Revised" License
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Code for generating Movi index in the create_indexes.sh #6

Open ammalabbasi opened 8 months ago

ammalabbasi commented 8 months ago

Thank you for putting together this repository for exhaustive host depletion! I am in the process of setting it up to run on my cancer samples. I noticed that the create_indexes.sh script (in the main branch) does not include code for generating the Movi index for the pangenomes. Is this code provided somewhere else in the repository that I might have missed?

Thanks, Ammal

lucaspatel commented 8 months ago

Hi Ammal,

Thanks for your interest in our pipeline. Generating Movi indexes can be a bit system-specific. Basically, you'll want to run the preprocess_ref.sh script as detailed in the Movi build instructions. 

bash /path/to/movi/preprocess_ref.sh default /path/to/assemblies.txt /path/to/out/folder

I also created a template build script in the scripts folder where you can replace the paths with your specific inputs. This script is SLURM compatible, and I do suggest you use the job scheduler for this as the runtime can be in the hours to days.

I hope this is helpful. Please let me know if you have further questions.

Thank you, Lucas

ammalabbasi commented 8 months ago

This is very helpful! Thank you so much!