-
Is there any possibility to identify plasmids in the main contig so even if it's labelled as chromosome? I need to evaluate the correctness of different assemblies and would therefore like to determin…
-
### Objectives
Train fine-tuned versions of gLM2:
- [x] Version 0 (v0): Initial fine-tuning and qualitative eval (completed).
- [x] Version 1 (v1): Fine-tuning with augmented training data accoun…
-
Hello,
I am interested in running RFPlasmid on an Enterobacteriaceae dataset and I see there is a precomputed database for it.
However, I am wondering whether it would not be wise to create an u…
-
Dear Bakta team,
Thank you again for a great tool! I am annotating the plasmid genomes of interest, and some of them are shorter than 100000 characters which is giving the following error-
`/opt…
-
Hi, I have a question regarding the --enable-score-calibration flag. I understand that it considers the composition of the sample to output a 'real' probability, e.g. plasmid score of 0.4 would mean t…
-
The _plasmid.gfa files doesn't contain typical gfa-data. Therefore I'm not able to open it with Bandage.
-
Related to #175
tldr: importing Euroscarf plasmids throws parsing errors. We should decide how to deal with them (handle or pass) to extract header information and support Euroscarf plasmids.
I …
-
### Objectives
- Develop and evaluate alternative plasmid embedding methods to serve as baselines for the OpenPlasmid dataset
- collaborate on establishing metrics
- related to #1
### Tasks
- …
-
Hi Antonio,
I had a question about calibrated aggregated classification scores output by geNomad. If I run a metagenome assembly through genomad, would it be appropriate to use the calibrated aggre…
-
Hi,
When classifying some Refseq sequences I noticed that some plasmids are being classified as virus. For example the reference assembly of Klebsiella pneumoniae (https://www.ncbi.nlm.nih.gov/data…