FAQ
No — Mycotools requires that an annotation accompanies an assembly.
Currently, Mycotools removes GFF entries whose type field falls outside the set outlined in the MTDB standard. Curation will be reworked to generally accommodate non-gene-derived GFF types.
Mycotools attempts to dereplicate fungal genomes between NCBI and MycoCosm, but some entries are duplicated because no obvious, parsable link exists between the two sites. For example, "Fibularhizoctonia" at GenBank will not be dereplicated with "Fibulorhizoctonia" from JGI.
A manually curated dereplication file is planned to handle these entries.
Some genomes are contaminated or incorrectly identified, so taxonomy assignments may be incorrect if the genus is mislabeled or the NCBI taxonomy is outdated. To correct a misidentified genome, change its genus column to the appropriate genus, then update the taxonomy:
mtdb update -t