Comments (4)
Actually, Bakta was designed and developed to annotate isolated bacterial genomes. In particular, the database comprises bacterial protein coding genes, only. Also, there are currently no options/parameters to surpass archaeal taxonomic information to 3rd party tools of the workflow, e.g. tRNAScan-SE.
Since bakta now has several huge advantages compared to prokka (e.g. pyrodigal and circos plots), is there any chance for an archaea-mode in the future, or is this design decision final?
from bakta.
Actually, Bakta was designed and developed to annotate isolated bacterial genomes. In particular, the database comprises bacterial protein coding genes, only. Also, there are currently no options/parameters to surpass archaeal taxonomic information to 3rd party tools of the workflow, e.g. tRNAScan-SE.
Regarding metagenomes:
For sure, a very interesting question. I haven't tried it yet but I'll put it on the list and will look into this.
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Hey @richardstoeckl, thanks for this follow-up question which gets asked more and more often. I totally see the point in this - I just haven't come up with a decision whether it's better to either add an archaea mode to Bakta or to start a new distinct project, maybe archa?
A distinct project would be highly-inspired by Bakta itself sharing a lot of code but would provide room for important distinctions we might have to make, both now and in the future. However, this would induce a lot of code duplication which could only be mitigated and handled by starting a 3rd library project.
In conclusion, yes there is definitely a chance for a "bakta-like" archaea annotation solution - I'm just not yet quite sure what might be the best way how to do it. For now, I rather tend to the 2nd idea of a distinct project.
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A quick follow-up:
Yes, Bakta works absolutely fine on bacterial metagenome-assembled genomes. Actually, due to its large and taxonomically untargeted database, it has a competitive edge compared to Prokka.
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Related Issues (20)
- Bakta run times on cluster HOT 4
- Downgrading dependencies is needed when installing bakta from conda HOT 2
- Roary is not working with bakta-generated gff3-files HOT 1
- KEGG annotations - the number is much lower number than expected HOT 4
- Possible issues running bakta in Singularity HOT 1
- Name and Product don't match Dbxref HOT 3
- Make the --region parameter better match the output of PGAP HOT 8
- tRNAscan-SE slow with multiple threads HOT 3
- PSC failed! diamond-error-code=-11 HOT 2
- Bakta Web Does Not Work HOT 6
- Diamond Error -9 HOT 3
- Is there a way to deactivate the overlap detection so bakta does not filter my input proteins? HOT 3
- Inquiry on CDS annotation HOT 2
- pyhmmer not found HOT 14
- pyrodigal has no attribute 'OrfFinder' HOT 11
- CRISPR prediction assertion error HOT 1
- (Re-)Generating bakta outputs from the JSON only
- Bakta web version ignores translation table change HOT 1
- reproducibility - amrfinderplus-db HOT 4
- Issue with trnascan-SE and bakta v1.9.4 HOT 1
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