FAQ

Can I add assemblies without annotations to MTDB?

No, Mycotools requires that an annotation accompanies an assembly

Can I include non-standard GFF types?

Currently, Mycotools will remove GFF entries that do not have a type field within the set outlined in the MTDB standard. In the future, Mycotools curation will be reworked to generally accomodate non-gene derived GFF types.

Does Mycotools comprehensively remove duplicate genomes?

While Mycotools attempts to dereplicate fungal genomes between NCBI and MycoCosm, some examples will be duplicated due to no obvious, parsable link between the two sites. For example, the genome for "Fibularhizoctonia" at GenBank will not be dereplicated with "Fibulorhizoctonia" from JGI due to the overlapping name.

There are plans to initialize a manually-curated dereplication file to handle these entries.

Some genomes are mislabeled, is there a way to correct their taxonomy?

Some genomes are contaminated or incorrectly identified, so some taxonomy assignments may be incorrect if the genus is mislabeled or the NCBI taxonomy is outdated. To correct misidentified genomes, change the genus column associated with it to the appropriate genus, then run mtdb u -t to update the taxonomy.