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Hi,
I recently annotated phages with phanotate in an environment where tRNAscan-SE was installed. Therefore, tRNA masking did use tRNAscan-SE. However, in my final NCBI submission I also added tRNA p…
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I'm having a issue when requesting to a graphdb endpoint, the reponse is always in srx format (application/sparql-results+xml) instead of srj format (application/sparql-results+xml).
I think the is…
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Hi here,
When I run VIBRANT on a metagenomics, it came across an error. But the output file of this metagenomics is complete. I wonder if this error will influence my identification results.
Here is…
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Looks great! I'd suggest a couple of improvements:
1. I would recommend you build trees using amino acids, rather than nucleotides unless you know you are comparing very similar phages.
2. You co…
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Currently, all sequences are considered as viruses that are reported as "phages" by PPR-Meta. However, we can additionally filter by a "phage score" provided by the tool:
```
Header,Length,phage_…
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Hi Kraken2 developers/community,
I recently built a large Kraken2 database with genomes from the NCBI RefSeq database. I added genomes regardless of assembly level and limited it to 1 assembly per …
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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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Hi deprekate,
I have used Phanotate but I am not sure what the output means. I ran it through a single metagenomics-assembled genome (MAG), and got multiple start and stoping codon frames in one si…
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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…