Taxonomy assignment from draft genome

Question

[Morgan S.]

Hi,

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.

[5heikki]

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

Answer 1

[lakhujanivijay]

You can give KAIJU a try. And use NCBI BLAST nr +euk - as above, but also including fungi and microbial eukaryotes option

Paper link is here

You can also use standalone version which could be downloaded here