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When a path not containing BLASTi is passed as `-b`, the following occurs.
```
$ ./MetaPhinder.py -i phage_genomes/phages_1_hr.fsa -b ./no/blast/here -d database/ALL_140821_hr
parsing commandline…
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- **Patric database** was found from
Guglielmini, J., Bourhy, P., Schiettekatte, O., Zinini, F., Brisse, S., & Picardeau, M. (2019). Genus-wide Leptospira core genome multilocus sequence typing for …
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Hi,
I am currently applying PropagAtE (default parameters) to gut metagenomic data and I am struggling to understand which filters to apply to the output .tsv files. I see that in the output .tsv f…
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Frameshift aignments are very useful for Nanopore data, where indels are common. It can also be used for virus-related research, as [some phages have conversed programmed frameshifts](https://www.cell…
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In case of missing `translation` qualifier in CDS features, the amino acid sequence is not generated by `interested_gene_generation.pl`.
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- **Organizational Page**: [Pathogens](https://github.com/NCEAS/open-science-codefest/wiki/Pathogens)
- Proposer: Bill Mills
- Field: Genomics (particularly WRT to pathogens)
- Computing: Python
- Lo…
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Hi,
Thanks for your pipeline for macro- and microdiversity analyses. It seems very helpful to my research. However, i have two major issues which need to be addressed.
1. I noticed that this pipel…
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* pharokka version: 17v
* Python version: 3.10
* Operating System: linux
### Description
Wondering if there is a quick fix for this?
To make the genome plot linear?
Just a quick fix. The ci…
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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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Dear Authors. Could you clarify please.
Is there a stronger threshold for the identification of eukaryotic viruses? Because those contigs, which according to the program belong to eukaryotic viruses …