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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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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364
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Hi, I have four more questions.
1. You defined five types inovirus in the result files: prophage, complete, integrase, DR, tRNA. But the type, complete, seems have no att sites. Are the complete …
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Hello @KrisKieft,
Thank you for developing such a great tool.
I want to apply PropagAtE to bacterial SAG data.
Could it be possible?
If there is anything I should be aware of, I would appreciat…
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Hi,
I have similar questions with Issue26(https://github.com/apcamargo/genomad/issues/26#issue-1796936020). But I have a large number of assemblies to explore for prophages using genomad (It could …
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Hi ,i have a doubt.
Actually i encountered a problem that some tandem insertions appeared,which have been talked about in previous questions. Here in my results, many multiple pI next to each other ,…
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Hello,
According to the paper, INPHARED should only include genomes producing virions:
> We also assume the genomes are from phages that have been shown to produce virions and are not prediction…
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We have been working hard on a database and some [cool demos](https://github.com/phageParser/phageParser/tree/master/demos) of analysis you can do with it. Our dream is to build a web front end so tha…
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Just a suggestion for the [database build step](https://bioinf.shenwei.me/kmcp/database/#gtdb). Since the sample size is pretty big, it's worth using the [`--enable-score-calibration` in geNomad](http…
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Hi,
I got this error during VirSorter2 run (environmental metagenomes contigs):
virsorter run -i sequences_cdhit_metagenomes.fasta -w VIRSORTERvers2 -j 4 all -d /home/nico/miniconda3/envs/virsorte…