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Thanks for making such a great tool! It's super easy to run and exactly what I need for my project.
Can you explain what the difference is between "Unclassified" and just "Viruses" in the taxonomy …
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When Sequencing rows have no oligo or type or date queued/queued by filled in, they can still be set to "Ready to mix".
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Dear @j23414
I see that some of the sequences in all_sequences.fasta file have plasmid DNA as well and therefore are circular DNA and have length greater than 12000 bp. These include
```
AY243…
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The names of these make it unclear which type of entity each is meant to refer to. Based on child terms of the latter, I'm guessing that it refers to the actual molecules and the former refers to the …
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Thanks for the great tool!
https://github.com/phac-nml/mob-suite/pull/159 addresses unstable ordering when sorting contig-link counts.
When assigning contigs to clusters, it feels the priority s…
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Big question about this:
https://github.com/andrewgull/HeteroR/blob/4ceb4343af906519da771fc2dc1f3ecb30daf9ea/notebooks/modelling/features.qmd#L1184-L1192
Eventually, is this the same table you cre…
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Started an AWS Ubunutu 18.04 server.
Installed python.
Installed miniconda.
Ran `conda install -c conda-forge -c bioconda -c defaults prokka`
No apparent issues with install.
Try running `prokk…
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Very exciting pipeline!
I would like to use the first step, classify_xgb.py, to identify if a contig comes from a eukaryote. Where can I find a description of how to interpret the results from this…
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The current tRNA (SO:0000253) tree has children for each tRNA isotype plus 'mt_tRNA', but this arrangement has a few problems/deficiencies:
- doesn't clearly distinguish between cytosolic/mitochondri…
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Salmonella enterica CP053576 might be the incorrect entry and I'll need to double check that. It might be the plasmid of subspecies IV and not the chromosome.