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4.8 years ago
Morgan S. ▴ 80
I have two assembled and annotated draft genomes of non-model fungal species. Based on the previous 18S analysis, they were both found to be closely related to Penicillium.
Now that I have the genome, I wanted to assign taxonomy. What is your preferred way of assigning taxonomy from draft genome assemblies?
Thanks, Morgan S.
It depends how accurate the results should be. If you want something ultra fast you could try MASH against pre-sketched RefSeq. The slow way is to detect homologs between closely related species (e.g. ribosomal proteins) and build a tree from a concatenated trimmed alignment with e.g. RAxML and/or PhyloBayes