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I understand the need and will add a command line parameter to exclude uncultured/environmental sequences.
Meanwhile you can run oligotyping with --skip-blast-search option, and then use OLIGO-REPRESENTATIVES.fasta file separately to assign taxonomy to your oligotypes or search them agains NCBI's ref_seq database.
Dear Mr. Eren,
is it possible to adjust blast in your command line so that uncultured/environmental sample sequences are excluded?
Thanks a lot for oligotyping, great tool!
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