How to create custom DataBase for FCS-GX?

ncbi / fcs

Foreign Contamination Screening caller scripts and documentation

Other

88 stars 12 forks source link

How to create custom DataBase for FCS-GX? #40

Closed maruiqi0710 closed 1 year ago

maruiqi0710 commented 1 year ago

I want to set the mtDNA of a certain species as a database, and use FCS-GX tool to remove mtDNA from the (nuclear DNA) genome assembly of that species.

pstrope commented 1 year ago

Hi, We currently do not have any plans to add a feature for creating custom databases. Identification of non-contaminant organelle sequences is something we’re considering for the future, but isn’t currently implemented. For your genome assembly, running blast against the mtDNA sequences might get you to the desired result.