Earl Grey

Updated Earl Grey Release

Updates:

• Initial RepeatMasker step is now optional, with default being no RepeatMasker run. This provides more information for the do novo RepeatModeler run to generate better TE consensus models for a species of interest. If required, an initial RepeatMasker step can still be run using the -r flag, specifying the library required.
• New BLAST, Extract, Align, Trim process. Completely overhauled BEAT process to extend TE consensus sequences to their boundaries. No fuzzy ends are now observed, and consensus sequences are only extended if required, not once ends are reached.
• Clustering is now optional, with default being no clustering. TE library sequences can be clustered to reduce TE library redundancy. However, this can have adverse effects on the identification of subfamilies and of independently-transposing chimeric TEs, where members of the chimeric TE will be labelled as subregions of the larger TE, rather than a separate unit.
• New TE classification step. This is still homology based, but is now incorporated into the BEAT process above. This makes use of RepeatClassifier from RepeatModeler2 to classify newly-identified TEs after extension.