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Hi,
Thanks for making this tool! I'm a little curious as to how to correctly interpret the prophage/host ratio in the output file. In your opinion, would this value be valid to rely on? Or rather, …
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At the statistical stage I am getting the error:
"statistics.StatisticsError: mean requires at least one data point"
It comes from line 758
avg_h = statistics.mean(cov_h)
I think it's becau…
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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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**Related To**
- [ ] Bactopia
- [x] Bactopia Tools
**Is this related to a problem?**
A description of what the problem is. Ex. I'm always converting X to Y, cannot adjust parameter Z [...]
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Excited to use this tool. I think it will help me automate the process of determining active prophages.
I've got a bacterial genome I ran VIBRANT on whose name is 'ENA|CP000721|CP000721.1 Clostridi…
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Hi Simon,
I am new in the field of prediction of viral sequences. I am basically interested in detecting the number of prophages from bacterial genomes (including MAGs) and tested your VirSorter so…
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Current sets of prophages are probably highly redundant, should use some kind of CD-HIT like clustering procedure to get a set of unique prophage sequences
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Gene strand can be very useful to detect prophages, but it is currently lacking from the `.gb` files. Because of that, there's no way to benchmark a tool that leverages strandness using proteins/ORFs …
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Hi, I got some MAGs using the binning method. I have identified prophage in MAG, and want to analyze the activation prophage. First, the MAG includes some contigs other than the whole genome sequence …