Question: RepBase alternative for maker?
1
gravatar for Colaptes
17 months ago by
Colaptes50
Colaptes50 wrote:

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!

maker repbase annotation genome • 1.8k views
ADD COMMENTlink modified 17 months ago by Charles Warden8.0k • written 17 months ago by Colaptes50
2

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) .

ADD REPLYlink written 17 months ago by microfuge1.9k

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.

ADD REPLYlink written 17 months ago by Colaptes50

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

ADD REPLYlink written 17 months ago by microfuge1.9k
1

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.

ADD REPLYlink written 17 months ago by jean.elbers1.5k

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

ADD REPLYlink written 17 months ago by Colaptes50
1
gravatar for Charles Warden
17 months ago by
Charles Warden8.0k
Duarte, CA
Charles Warden8.0k wrote:

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

ADD COMMENTlink written 17 months ago by Charles Warden8.0k
1

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.

ADD REPLYlink written 17 months ago by Colaptes50

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

ADD REPLYlink modified 17 months ago • written 17 months ago by Charles Warden8.0k
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