Skip to content

Earl Grey v5.0.0

Latest
Latest
Compare
Choose a tag to compare
@TobyBaril TobyBaril released this 10 Oct 14:07
· 2 commits to main since this release
v5.0.0
38ca68d
This commit was created on GitHub.com and signed with GitHub’s verified signature.
GPG key ID: B5690EEEBB952194
Learn about vigilant mode.

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

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

Contributors

TobyBaril
Assets 2
Loading