Earl Grey v6.0.1

Full Changelog: v6.0.0...v6.0.1

Earl Grey v6.0.0

Earl Grey v6.0.0 is here!

There are some relatively large changes in this release, resulting in the jump to v6.0.0.

Importantly, Earl Grey has been updated to use Dfam version 3.9, with RepeatMasker 4.1.8 and famdb 2.0.1. This means that there is some extra configuration required to get the pipeline running. Upon first installation and running of Earl Grey, the pipeline will check whether RepeatMasker has been configured with the correct Dfam database partitions. If not, it will warn you, generate a script that you can modify and run to configure RepeatMasker, and provide instructions to stdout if you want to do this yourself.

Please take care to configure Earl Grey v6 with ALL required partitions. More information on the partitioning can be found at Dfam.org.

Earl Grey v5.1.1 will continue to work for those who are happy with Dfam v3.7, but we recommend upgrading to v6.0.0 to keep up to date with the latest improvements to the database.

What's Changed

• Earl Grey v6.0.0 by @TobyBaril in #188

Full Changelog: v5.1.1...v6.0.0

Earl Grey v5.1.1

What's Changed

• Patches for V5.1.1 by @TobyBaril in #177

Full Changelog: v5.1.0...v5.1.1

Earl Grey v5.1.0

• Updated to replace water with matcher to reduce memory consumption in divergence calculations in line with EMBOSS recommendations

Earl Grey v5.0.3

Full Changelog: v5.0.2...v5.0.3

Earl Grey v5.0.1

• Patches to repair missing options that have been deprecated in RepeatModeler2. No major changes to the pipeline.

What's Changed

• Patches for RepeatModeler Updates by @TobyBaril in #164

Full Changelog: v5.0.0...v5.0.1

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