Earl Grey v4.0.3

Small bug fixes and patches

• Softmasking
• Thread count in initial RepeatMasker (optional)
• README permalinks to DFAM3.7 whilst we await a RepeatMasker Conda release for 3.8

Earl Grey v4.0.2

Bug fixes and patches related to softmasking and final filtering of TE annotation files.

Earl Grey v4.0.1

Small bug fixes and improvements.

• Patched issue with soft mask flag not being parsed properly
• As the conda environment is now the recommended install, and by default uses the rmblast search engine, the number of threads given to Earl Grey by -t is now divided by 4 for all RepeatMasker steps, as RepeatMasker with rmblast uses number of threads multiplied by 4, as each process uses 4 threads.

Earl Grey v4.0

New features incoming!

Thank you for using Earl Grey and for giving me suggestions on how I can make this tool better for your research purposes. It means a lot that you are choosing to use my tool, which has been my baby for a long time now! I have implemented some popular requests, and you can find information on these below.

• Added the option to generate a soft-masked version of the input genome after annotation defragmentation with -d yes.
• Removed the default behaviour of removing TEs <100bp in length. This is now an option implemented with -m yes.

Keep your eyes open for the new preprint that should hopefully appear soon!

Earl Grey v3.2.2

Added checks for users trying to run Earl Grey in biocontainers. Biocontainers do not come with a configured version of Dfam for RepeatMasker. Added a sanity check for Dfam configuration. If this is not configured, Dfam will be downloaded and configured so that the biocontainer will function correctly.

Earl Grey v3.2.1

Small bug fixes for using famdb.py in the conda environment, which is activated if the user requires masking of the input genome with existing repeats in Dfam and/or RepBase. Recommended to pull this update if you wish to use Earl Grey with the -r flag for intial mask.

Earl Grey v3.2

• Earl Grey is now in bioconda!
• This update has some small fixes for optional stages:
• clustering had an issue with finding the correct file, this has been fixed
• a new way to determine the latest output of TEstrainer has been implemented so that the latest file is always found in the event of a failure, without the user having to manage files.
• fixes in TEstrainer_for_earlGrey.sh, where there were relative file paths rather than full paths
• README has been updated with changes enabling compatibility with Mac in addition to linux systems

Earl Grey v3.1

Small changes to improve user experience.

• New Conda environment includes all R packages configured, so no need to add some extra bioconductor ones with a script anymore
• New Conda environment resolves all conflicts
• Altered configure file to prevent installation of unrequired R packages
• Altered TEtrim.py in TEstrainer as function has been deprecated in new BioPython

Earl Grey v3.0

• Scoring threshold reduced following validation with benchmarking on a simulated dataset. Reduced false negative rate by changing RepeatMasker scoring threshold from 400 to default, likely improving the detection of degraded/older elements.

Earl Grey v2.4

Update install_r_packages.R