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4 votes

Get a comprehensive list of virulence factors for certain or all pathogens?

I suggest that you are looking for a resource like VFDB (virulence factor database). That table does annotate by bacterial species, so you can filter as you like. You can download a description table ...
Maximilian Press's user avatar
2 votes

where to find pathogenicity metadata for E.coli genomes

you can use BacDive. This is the largest database for bacterial metadata.: https://bacdive.dsmz.de/ e.g. you can search for the sequence accession "NCTC8196" and you would get the metadata of the ...
user6331's user avatar
2 votes

error in random forest analysis

This question will be a little hard to answer without more information. For example, we will need to see your dataset (whole_root_pred), to decide why ...
Maximilian Press's user avatar
1 vote
Accepted

Regarding canonical analysis of principal coordinates (CAP) for linking microbial data with elements

I don't think that you can say that the 25% can be said to relate to the chemical variable specifically; rather, that 25% is the variance that is explained by all constrained axes. While these axes ...
Maximilian Press's user avatar
1 vote

kraken2 to OTU table creation

You need to run Bracken to the Kraken2 report output to estimate abundance.
zorbax's user avatar
  • 769
1 vote

repophlan script to download bacterial genome

UPDATE 2: new log posted take-home message: I think it is working, it's just that a few errors happen sometimes when downloading things from big databases. It looks like there are a few warnings or ...
Maximilian Press's user avatar
1 vote

Optimum parameters for genome assembly via canu

The canu parameter reference guide is always a good place to start. It would help to know a little bit more about what your assembly looks like. E.g. what is your n50, n90...? What is your dataset ...
Maximilian Press's user avatar

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