I am very new on bioinformatics. I will be running MinION in the near future and I have a question which I still couldn't figure out the solution. As part of the post sequencing analysis of the MinION data, I wish to remove parts of the reads that have been mapped/assigned to a custom database (in this case will be the host genome data) so that I am left with the non-host reads for further analysis. Any idea which software can do so?
Thank you very much in advance!