I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements.
This works well enough, and seems to be the de facto standard in the field.
However, there are two issues with the use of RepBase, which is why I (and others) have been looking for alternatives (so far without success):
RepBase isn’t open data. Their academic license agreement includes a clause that explicitly forbids dissemination of data derived from RepBase. It’s unclear to what extent this is binding/enforceable, but it effectively prevents publishing at least some of the data I’m using and generating. This is unacceptable for open science.
- Subordinate to this, the subscription model of RepBase also makes it impossible to integrate RepBase into fully automated pipelines, because user interaction is required to subscribe to RepBase, and to provide the login credentials.
RepBase is heavily manually curated. This is both good and bad. Good, because manual curation of sequence data is often the most reliable form of curation. On the flip side, manual curation is inherently biased; and worse, it’s hard to quantify this bias — this is acknowledged by the RepBase maintainers.