Comments (1)
Yes you can substitute your own databases. Check out the MMSeqs documentation on downloading or creating your own databases: https://mmseqs.com/latest/userguide.pdf
At the moment, you would need primary and secondary aa and nt databases. For the aa databases, read the bit on Creating a seqTaxDB; it's pretty easy if you're using uniprot accessions/databases. For the nt database, here's an example of how we do it:
https://github.com/shandley/hecatomb/blob/v0.2.2/accessory/create_mmseqs_viral_nt_taxaDB.sh
If you didn't want our iterative search strategy (where we use the smaller aa and nt databases to prefilter, before putting the hits through the larger secondary databases) then that would require more extensive changes to the pipeline rules themselves. Was there something specific you wanted to try?
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Related Issues (20)
- 98, 99% Failure Issue HOT 1
- ModuleNotFoundError: No module named 'attrmap' HOT 1
- Errors in newest version 1.3.0 HOT 15
- Placeholder of length limit HOT 3
- hecatomb combine not working HOT 3
- hecatomb.config.yaml HOT 1
- Hecatomb not working ( secondary aa taxonomy) HOT 3
- ERROR: Snakemake failed HOT 4
- Long reads support HOT 5
- Failed job in processing secondary_nt_calc_lca step HOT 2
- Another error in processing mmseqs_contig_annotation HOT 1
- Hecatomb test error
- Process secondary_nt_calc_lca failed HOT 1
- Solving OSerror Issues in a WSL Environment during the megahit step. HOT 2
- bigtable.tsv column question HOT 1
- Filtering out host (human) genome beforehand? HOT 3
- No rule to produce assembly HOT 5
- add-host is failing on mask_host HOT 3
- out-of-memory error during population_assembly.flye, STAGE: repeat HOT 2
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