[maker-devel] Repbase subscription

[Taslim, Cenny]

Hi,

 

I just have a quick question before spending time to install maker. Now that Repbase requires active subscription as of April 2019, it is possible to run maker without Repbase?

 

Thanks,

Cenny

[Carson Holt]

Yes. Do a manual install of RepeatMasker with HMMER as the aligner and Dfam as the reepeat database (free). Run RepeatModeler to get an assembly specific repeat dataset and give that to MAKER. The combination of the two will allow you to mask sufficiently for the annotation.  If for any reason you want to classify the repeats into families for further analysis rather than just mask them out, then you want a RepBase subscription.

—Carson

_______________________________________________
maker-devel mailing list
maker...@yandell-lab.org
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org

[Fields, Christopher J]

A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal).  For example, this one from the U. of Illinois, which requires login to access.  

chris

[Taslim, Cenny]

This is good to know. Unfortunately our university library does not have a Repbase license.