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gbouras13 / pharokka

fast phage annotation program
MIT License
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what gene should we use to put at +1 in a Stx-phage assembly #306

Closed splaisan closed 7 months ago

splaisan commented 7 months ago

Hi George, All,

disclaimer: sorry but I am not a bacteriologist nor a virolog ;-)

I do not find 'terminase' genes in my circularStx- phage assemblies although they are described in Pinto et al 2021 for this usage! Is this normal in a non-integrated form or is it due to flye

I usually use circlator fixstart to put DnaA at +1 in bacterial assemblies and would like to also show nice maps for my phages.

Do you have a recommendation for the choice of the first gene to show on a bacteriophage map? Is the first shiga gene a good option?

thanks for your feedback and knowledge

gbouras13 commented 7 months ago

Hi @splaisan,

I’ll come back with a more lengthy explanation tomorrow (it’s late in Australia), but I have just the tool for you I think :)

https://github.com/gbouras13/dnaapler

splaisan commented 7 months ago

Hi George,

Both dnaapler and pharokka rock, they need more exposure (you should consider making a bioXiv paper of some kind to promote your work ! I ran dnaapler phage based on your very clear doc and it seems to have worked like a charm. I will most likely drop circlator fixstart from now on and use dnaapler for all my reorientation needs. Finishing an assembly with reorientation is a real must, too often I see random circles published and very hard to compare by eye.

Thank you so much for your nice work and clear tools.

gbouras13 commented 7 months ago

Thanks @splaisan for you very kind words - I am trying to get Dnaapler published at JOSS, hopefully won't be too long :)

Another thing is that you can actually run Dnaapler within pharokka if you use --dnaapler - the reoriented phage is in the output directory.

If you do bacterial assemblies too, you may be interested in my tool Hybracter (https://github.com/gbouras13/hybracter) - a preprint for this one is coming very soon, and I'd love feedback if you try it out.

George

splaisan commented 7 months ago

Thanks George,

I indeed saw the option after receiving your message. I will include it next time. I did not know yet what dnaapler was then.

I can easily try Hybracter as I just performed bacterial assemblies which I rotated with circlator. I will redo this step and let you know.

cheers