Earl Grey

☕ Earl Grey v7.0.0 is here! Some long-awaited changes in this release—thank you for your patience while I found the time to properly test and implement them. 🐞 RepeatCraft fixes First, I've fixed an issue in RepeatCraft where distal TEs could be grouped erroneously. This occurred in rare edge cases where the internal counter failed to iterate when new distal copies of an existing TE were detected on the same contig. This should now be fully resolved. 🧬 Fully nested TE handling (major update) I've also completely revamped the Earl Grey post-processing and summary steps to properly deal with Fully Nested TEs. Partially overlapping TEs are handled as before, following the approach described in the original Earl Grey paper. Fully nested TEs are now identified using a new iterative process: The GFF is scanned for nested TEs These are labelled and stored in a separate file The nested TE is removed and the GFF is re-scanned to detect deeper (multi-level) nesting This continues until no new nested TEs are found 📊 Changes to coverage and summaries (important) Nested TEs are no longer included in the TE coverage calculation used to generate the pie chart in the summaryFiles directory. Instead: Summary tables now include new categories showing how many base pairs are comprised of nested TEs These base pairs are not counted toward Total Interspersed Repeats, as doing so would result in double-counting genomic space. ⚠️ This represents a substantial change from previous versions, so please be aware of this difference when upgrading to v7. The output table summary now has the following format: |TE Classification | Coverage (bp)|Copy Number | % Genome Coverage| Genome Size| TE Family Count| |:-------------------------------------------------|-------------:|:-------------|-----------------:|-----------:|---------------:| |DNA | 80886|326 | 0.7607795| 10631990| 326| |DNA-nested | 1449|29 | 0.0136287| 10631990| 29| |Rolling Circle | 8022|31 | 0.0754515| 10631990| 31| |Rolling Circle-nested | 0|0 | 0.0000000| 10631990| NA| |Penelope | 112822|812 | 1.0611560| 10631990| 812| |Penelope-nested | 1268|13 | 0.0119263| 10631990| 13| |LINE | 132133|426 | 1.2427871| 10631990| 426| |LINE-nested | 1268|13 | 0.0119263| 10631990| 4| |SINE | 0|0 | 0.0000000| 10631990| NA| |SINE-nested | 0|0 | 0.0000000| 10631990| NA| |LTR | 0|0 | 0.0000000| 10631990| NA| |LTR-nested | 0|0 | 0.0000000| 10631990| NA| |Other (Simple Repeat, Microsatellite, RNA) | 189999|4241 | 1.7870502| 10631990| 4241| |Other (Simple Repeat, Microsatellite, RNA)-nested | 1225|34 | 0.0115218| 10631990| 34| |Unclassified | 274026|1291 | 2.5773726| 10631990| 1291| |Unclassified-nested | 0|0 | 0.0000000| 10631990| NA| |Total Interspersed Repeat | 607889|2886 | 5.7175468| 10631990| NA| |Non-Repeat | 10024101|notApplicable | 94.2824532| 10631990| NA| In the final GFF output, nested TEs are clearly labelled with a nested=FULLY_NESTED attribute in column 9, enabling quick identification and downstream filtering. NC_045808.1 Earl_Grey Simple_repeat 51840 51871 14 + . ID=(CGCA)N_33;Name=(CGCA)N;tstart=1;tend=31;shortte=F;nested=FULLY_NESTED-ROUND1 As always, thank you to the TE community for your enthusiasm in using Earl Grey, and for your invaluable feedback and bug reports. I'll continue to incorporate improvements and fixes as quickly—and carefully—as possible. Happy New Year! 🎉 What's Changed Multiple Updates for Version 7: RepeatCraft BUGFIX, Implement Nested TE Labelling and Calculation Refinement by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/254 Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.3.6...v7.0.0