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Hello,
I have installed plasmidtron plus its dependencies as described in the readme file. However, I do not understand what input files should be. specifically, what are file_of_traits and file_of_…
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Hi there,
I've got a few bacterial assemblies in which I determined some plasmid sequences. I therefore wanted to try out Unicycler to figure out whether it would be able to optimize my Illumina-on…
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Having new organism on GGBweb is mandatory. A organism can have more then 1 element (locus= chr, plasmids). We already deal on the data side (locus columns). Now we need to deal on the UI side (front-…
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The following genomes did not download in Kalamari 5.3.3. I'm wondering if I need to replace these.
CP000927
CP000937
CP000949
CP000950
CP001010
NC_000907
NC_000915
NC_003454
NC_003888
NC_…
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- [x] add second scrubby step to keep chlamydia reads only
- [ ] consensus sequences:
- [x] use ragtag for scaffolding
- [ ] separate genome from plasmid
- [ ] collate genomes in single outp…
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Hi!
Thank you for developing such an interesting tool to identify plasmids.
So I did use the example's settings to perform a first analysis of the assembled contigs fasta file I have and I took a…
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Currently, adding a new container to a sample type prompts the creation of a new object type. There should be a way to assign pre-existing containers.
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Hello,
I did some test runs with the software, and I noticed that it could not discriminate between prokaryotic and viral sequences. As a result, it often classifies viral sequences as plasmids. I gu…
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Hi, I have run PLASMe on a dataset and have obtained the output fna file but the only csv file that is generated (called PLASMe_candidate.csv) is located in the TEMP directory and contains the informa…
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Is it possible to only download plasmids? NCBI Genome has a plasmid-specific page, but I don't see that option in ncbi-genome-download.
Don't know how easy this is?