Does lots of N bases affect the results?

[qingruoyu]

Hi, I wonder if the VPF used the -m option to mask the N bases when invoking prodigal. Because viral scaffolds are used for input, which contain many consecutive N bases, does this affect the results?

[bielr]

Hi,

Sorry, we haven't done any tests with that option. However I've just pushed a new flag "--prodigal-mask-n" that should allow you to try it by yourself if you need to. If you reach any conclusions would appreciate it!

[qingruoyu]

Great! Thank you very much for providing this option. I used the binary version you provided in issue #2, because some problems occurred when using VPF-class with stack. Could you provide the latest binary version? It's very concise and easy to use.

[bielr]

We do have an up-to-date Docker image. Does it work for you?

[qingruoyu]

Sorry, I don't have root access to install and use Docker. Most of the software is installed through conda.

[bielr]

In that case, I can suggest multiple rootless alternatives:

• Docker (in rootless mode)
• Podman (rootless configuration)
• Singularity (rootless configuration)

All of these require prior configuration from your sysadmin, but afterwards require no root access. We aren't publicly providing any standalone binaries because sadly we don't have all the time/resources to ensure that they work properly on multiple systems and configurations.

[qingruoyu]

Got it! Thanks for your suggestion.