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Hi,
I recently tried eggnog-mapper website to annotate my bacterial genome for COG analysis. From the resulting output I was using the column of COG_categories to calculate the number of genes annota…
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I am currently trying to run the demo with MetaPhage-0.3.3, I ran into a problem when executing the pipeline
```
Step 5 : /home/jm2338/miniconda3/envs/metaphage/bin/Scripts/Step_5_get_phage…
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Hi Rob,
I was really excited to see that someone is doing a comparison of different prophage tools. If you are still open to adding more tools for comparison, I hope you try my tool [Cenote-Taker 2…
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Hello! Thank you for your previous help. I now have a set of prophages identified by Prophage_tracer that I want to further investigate and I want to better understand the output files. I was hoping…
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Thanks for sharing the protocol. I have tried it for some prophage genomes, but most genomes can only have the taxonomic information in "class" level. Is there a way to get species/family level inform…
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First off - thanks for this tool!
i ran the workflow on the test dataset with no problems, but I've been trying to test it on some genomes we sequenced, and am getting an error at the interval findin…
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364
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I want to map reads to AMGs sequences to get AMGs abundance information. But I do not know how to get AMGs sequences file. I try to use identified protein ID to separate it from prodigal.ffn file. …
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Currently, reports are in one folder, which is very helpful, but there are 4 files (report_general.html, report_MGEs.html, report_resistance.html, report_virulence.html) separately and I found myself …
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[Phaster](http://phaster.ca/), an outside program that we're using to find prophages in genomes, is occasionally giving a weird error where the API request `requests.get(apiurl)` returns ``, then a fe…