RepBase alternative for maker?

Question

[Colaptes]

Hi there,

I'm doing a genome annotation of a non-model annotation using Maker and have a question about repeatmasking.

My institution does not have a license to use RepBase now that it requires a paid subscription. Is there a good alternative to using RepBase for repeatmasking within Maker? I have made a custom TE library using RepeatModeler and following the instructions included in the maker wiki's Repeat Library Construction-Advanced (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced). Would this be sufficient on its own for repeatmasking or is the RepBase database really required for maker to work well?

Thank you!

[microfuge]

Just in case your institution is an academic one you can register and get the download urls via email (takes about 2 to 3 days) .

[Colaptes]

Is this still the case after they added the new subscription model in April? After making an account I am redirected to a $1395 paywall to download RepBase with an individual academic license.

[microfuge]

Oh did not know. Did you use your institutional email address and not a personal one? They seem to be particular about it.

[jean.elbers]

My two cents...your miles may vary... I've included a custom repeat library made from RepeatModeler and just used Dfam that comes with RepeatMasker in the past. Note that I think MAKER 2.31.10 only works with RepeatMasker up to version 4.0.7 and not the newer versions at least that was the case the last time I tried.

[Colaptes]

Thanks! I will try maker with Dfam and the custom library then and see how it goes.

Answer 1

[Charles Warden]

I'm not sure what matters most for your specific project.

In general, I guess the issue that that you are working for a commercial company?

Otherwise, as mentioned above, the registration should be free for non-profits (but I don't remember exactly how long it look to create an account):

https://www.girinst.org/accountservices/register.php

[Colaptes]

As far as I have been able to find a subscription to RepBase now costs $1395 per year as of April for an individual academic license unfortunately. I made an account but when I go to the downloads page for repbase it redirects me to a paywall.

[Charles Warden]

That is strange.

I am already registered, but RepBase was free for me to use. Given that I only have one non-profit e-mail address, I can't really do a perfect test at this point.

However, I tested creating an account with my Gmail address. At the first step, the registration said that it was successful. I haven't gotten an e-mail yet (the other responses indicate that there can be a bit of a delay). I can already sign in, but I think I need an additional code to confirm whether I can still download the files for free.

Additionally, I also see this message:

https://www.girinst.org/repbase/sub_announcement.html

I certainly think RepeatMasker needs to be freely available. If a RepBase subscription causes a problem with that, then I think some alternative strategy should be defined (or at least leave the last freely available version for everybody to download).

For what it is worth, I have added that to a blog post (which I expect to further revise):

http://cdwscience.blogspot.com/2019/07/personal-thoughts-on-collaboration-and.html