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There are a number of useful metagenomics tools out there, including Centrifuge and Kraken2, as @gringer has mentioned. Also, FWIW, the WIMP tool from ONT, a Centrifuge based metageonomic classifier, does include fungus sequences derived from RefSeq, though it may not include the species you are looking for. If you want to use NCBI BLAST, you could split ...


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I've found Centrifuge and Kraken2 to be useful for species classification. There are pre-prepared databases that include Fungi, e.g. see here for the Kraken 2 "PF" database, which is the Standard database plus protozoa & fungi. Can't really provide much more help than that with more information about what you've done. You'll need a computer ...


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