Earl Grey v5.0.0

Earl Grey v5.0.0 is here!

This release incorporates the incremental improvements made throughout the life of version 4.

It is now possible to run some subroutines in Earl Grey (run either of these new commands with -h to see a list of options):

• earlGreyLibConstruct can be used to run Earl Grey for de novo TE detection, consensus generation, and improvement through the BEAT process. The output will be the strained TE consensus sequences, which can then be used for subsequent annotation. This is useful when you want to make a combined library from the libraries of several different genomes, where it is no longer required to waste time running annotations. Once the libraries are generated and you have curated them, you can then run the next step in isolation (next point!).
• earlGreyAnnotationOnly can be used to run the final annotation and defragmentation steps in Earl Grey. This is useful if you have already run the BEAT process and have a library of de novo TE consensus sequences that you would like to use to annotate a given genome. This script is also compatible with the -r flag to take known repeats from the databases used to configure RepeatMasker in addition to the custom repeat library.
• EXPERIMENTAL FEATURE: I have also added an option to run HELIANO for improved detection of Helitrons, which are notoriously difficult to detect and classify using homology methods. This can be implemented by adding -e yes to the command line options after upgrading to v5.0.0. Currently, HELIANO annotations replace those which they overlap following the RepeatMasker run, which is performed during defragmentation (in a similar way to full-length LTRs being dealt with in RepeatCraft). Feedback is welcomed on this implementation, and I am continuing to test and improve the implementation of HELIANO within Earl Grey.

Thank you for your continued support and enthusiasm for Earl Grey!

What's Changed

• Add updates to README by @TobyBaril in #146
• Updates for Version 5! by @TobyBaril in #150

Full Changelog: v4.5.0...v5.0.0

Earl Grey v4.5.0

1. Edge case fixes in TEstrainer
2. New earlGreyLibConstruct tool to generate de novo libraries for manual curation starting point

What's Changed

• Patches for v4.4.6 by @TobyBaril in #141

Full Changelog: v4.4.5...v4.5.0

Earl Grey v4.4.5

Fixing of edge cases in divergence calculator and issues with fai creation linked to multithreading.

Full Changelog: v4.4.4...v4.4.5

Earl Grey v4.4.4

Fixes to the divergence calculator - prevent crashing of script if plot is empty

Earl Grey v4.4.2

Bug fixes in the divergence calculator scripts.

Earl Grey v4.4.1

• Updated divergence calculator with fancy plots and a summary table showing TE divergence estimates by family (can be found in summaryFiles at the end of a successful run
• New experimental earlGreyLibConstruct script: generate a de novo TE library and BEAT it, but skip the annotation steps. Useful for those pangenome peeps out there, as well as those that want to create libraries on an individual-level before combining, manually curating, and then annotating with a final library later on.

Earl Grey v4.4.0

• Updates to the TEstrainer pipeline due to updates in required python packages
• Updates to the divergence pipeline due to changes in dependencies

Earl Grey v4.3.0

What's Changed

• Patches for Release 4.3.0 by @TobyBaril in #114

Full Changelog: v4.2.4...v4.3.0

Earl Grey v4.2.4

Small patches for stability
updates to readme

v4.2.3

• Patch fixes on new divergence plots

Full Changelog: v4.2.2...v4.2.3