Best way to go about making a custom database?

[Justin Wright]

Hello CLARK users,

I just have a quick general question regarding the utilization of this tool. I have managed to use this tool successfully for generating Viral annotations for my metagenome datasets, however I am having trouble properly utilizing this tool for a custom database annotation. Essentially, my hope is to identify fungal reads within my metagenome samples, but I do not know the best way of going about this. I have attempted to download the UNITE database and map against that, but did not manage to get any annotation hits, despite not getting an error message. It seems this may not be the best database for this tool however, so my question is where should I look for Fungal genomes to download and map against. Is the NCBI ftp site best? If so can someone point me in the direction of the appropriate FTP site so I can ensure that my input is formatted correctly?

I would appreciate any assistance!

Thank you,

Justin Wright

[Rachid OUNIT]

Hello Justin!

Thank you for your interest and I think you have here a great question.

This could actually lead to new feature when setting the database.

What would be the (default/standard) list of fungi genomes that CLARK should download if it could do it for you automatically? 

Cheers,

Rachid

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