Use Pyrodigal as Prodigal alternative

[lfenske-93]

Hi,

Since GTDBtk is using Prodigal, I was wondering if maybe you have thought about switching to Pyrodigal?

In case you haven't came across the Prodigal bug yet: A typo in the node scoring function causes Prodigal to apply a score penalty to any candidate gene located on the reverse strand. It's patched already, but there's no official patch release: hyattpd/Prodigal#88

I think since release 2.0.0 Pyrodigal is a reliable, faster and most important actively maintained version of or successor to Prodigal.

You might want to think about giving it a try. 😉

Greetings,
Linda

[donovan-h-parks]

Hi Linda,

Thank you for bringing this to our attention. We are investigating further. Do you have any sense of how much this bug impacts Prodigal results?

Cheers,
Donovan

[lfenske-93]

Hi Donovan,

as far as I know it affects the overall gene prediction, so that some genes are predicted in the wrong places and others may not be predicted at all.

We stumbled across this some time ago and one of my colleagues then made a major comparison between Prodigal and Pyrodigal: https://github.com/jhahnfeld/prodigal-pyrodigal-comparison

It is definitely worth taking a closer look at Pyrodigal, as it is becoming more and more popular, many people and tools are currently switching to it.

Greetings,
Linda