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([helper_functions.py](https://github.com/linsalrob/PhiSpy/blob/7de1d69fbe61224d2c7c29866ea3a3b29c7ee948/modules/helper_functions.py#L49))
The current number is 30, which seems a little high, as wh…
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What is the difference between the 'Phages, Prophages, Transposable elements' and 'Phages, Prophages, Transposable elements, Plasmids'. How are 'Phages, Prophages, Transposable elements' incorporated …
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Hi,
I'm trying to install VirSorter on our HPC cluster and have encountered an issue when testing on a bacterial genome which I know has several prophages and those were detected using VS on my loc…
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I couldn't find this information in the publication.
Thanks,
Stephen
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Hello! I'm a breseq noob and haven't been able to figure out what my issue is. My fastq files are a little unique so I'll describe them first:
To save money, I've paired single E coli and phage lam…
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Hi! I just observed a possible issue where a predicted prophage sequence's stop is larger than the actual contig size:
### Test assembly:
[kleiner_2015.fasta.gz](https://github.com/simroux/VirSo…
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I can't seem to find genomic coordinates of prophages anywhere in the output files. Could you point me in the right direction?
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### Background
As additional validation step we can check how many of predicted viral sequences we can blast in a database of viral sequences including metagenomes: https://img.jgi.doe.gov/vr/
###…
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Hello,
while testing phigaro-2.2.1 I encounter the following problem
```
[gensoft@e211aa82115c 0.2.1.8-3]$ phigaro -f ../../datas/phigaro/Bacillus_anthracis_str_ames.fna -o out.phg -p --not-op…
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I'm having issues getting virsorter to run on some ~300 genomes, using conda and the wrapper script. I'm unable to use the docker image unfortunately on our cluster. The first error in the error log f…