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Dear tseemann,
I want to only annotate plasmid sequences from an assembly file (contig.fa). Can you please guide how can i do this?
Thanks
J.A
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Goldenbraid plasmid data and maps are also available on this google drive
https://drive.google.com/drive/folders/1QIsJKr4SZyUiKJATi9qJE6ns-60s-K6u
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Hello Geroge, such a great tool you have in hybracter!!
I have been using it to assemble some ONT only genomes, without using medaka, and I have seen that even though dnaapler is run on the chromos…
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Settle on an analysis plan for plasmid data. Report:
```
PLASMID_FAMILY
PLASMID_BEST_MATCH
PLASMID_COVERAGE
PLASMID_SNVS_TO_BEST_MATCH
PLASMID_CARBAPENEMASE
PLASMID_INC_GROUP
```
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I have worked with several plasmids coming from [Euroscarf](http://www.euroscarf.de). I think it would be good to support importing these plasmids as a source!
However, note that I opened one of th…
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note reads "Note: 'cloning vector role' is really a function. Should be dealt with globally"
Reported by: mcourtot
Original Ticket: [obi/obi-terms/365](https://sourceforge.net/p/obi/obi-terms/365)
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I'm not sure how to set the identities of owned objects while preserving the IDs from SBOL2. When I try to set the identity of a `Cut`, for example:
```python
import sbol2
from sbol_utilities imp…
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Hi
I have noticed the problem of #138 quite some times in many bacteria ncluding E coli, and Clostridia. Plasmids found in Illumina assembly and detected in the lab (!), disappeared in Unicycler …
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The layout of labels in plasmid view looks rather horrible and needs fixing. This is mainly a problem when there are very many labels. Much too many labels will also throw an error.
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Running:
`
asm = Assembly((pdonr_plasmid, insert), limit=6, max_nodes=10)
`
gives me:
`
TypeError: Assembly.__init__() got an unexpected keyword argument 'max_nodes'
`
Is this intended, or sho…