earlgrey - Earl Grey v6.3.3

What's Changed

• Earl Grey v6.3.3 - Small Patches by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/230

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.3.2...v6.3.3

- Python
Published by TobyBaril 6 months ago

earlgrey - Earl Grey v6.3.2

• Small bug fixes to TE family quantification table

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.3.1...v6.3.2

- Python
Published by TobyBaril 8 months ago

earlgrey - v6.3.1

Bugfixes in file parsing with new GFF changes

- Python
Published by TobyBaril 8 months ago

earlgrey - Earl Grey v6.3.0

• Changes to GFF naming to be compatible with browsers (ID is now unique, Name is TE family field).
• Stop checking for IS elements in RepeatMasker runs

What's Changed

• V6.3.0-dev by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/215

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.2.0...v6.3.0

- Python
Published by TobyBaril 8 months ago

earlgrey - Earl Grey v6.2.0

What's Changed

• Resume TEstrainer by @nikostr in https://github.com/TobyBaril/EarlGrey/pull/202
• pull into 6.2.0 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/207
• Earl Grey V6.2.0 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/208

New Contributors

• @nikostr made their first contribution in https://github.com/TobyBaril/EarlGrey/pull/202

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.1.1...v6.2.0

- Python
Published by TobyBaril 9 months ago

earlgrey - Earl Grey v6.1.1

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.1.0...v6.1.1

Small patches for low-thread runs

- Python
Published by TobyBaril 9 months ago

earlgrey - Earl Grey v6.1.0

What's Changed

• V6.1.0 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/201

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.0.3...v6.1.0

- Python
Published by TobyBaril 9 months ago

earlgrey - v6.0.3

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.0.2...v6.0.3

- Python
Published by TobyBaril 10 months ago

earlgrey - Earl Grey v6.0.2

What's Changed

• V6.0.2 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/195

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.0.1...v6.0.2

- Python
Published by TobyBaril 10 months ago

earlgrey - Earl Grey v6.0.1

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v6.0.0...v6.0.1

- Python
Published by TobyBaril 11 months ago

earlgrey - 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 https://github.com/TobyBaril/EarlGrey/pull/188

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v5.1.1...v6.0.0

- Python
Published by TobyBaril 11 months ago

earlgrey - Earl Grey v5.1.1

What's Changed

• Patches for V5.1.1 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/177

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v5.1.0...v5.1.1

- Python
Published by TobyBaril about 1 year ago

earlgrey - Earl Grey v5.1.0

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

- Python
Published by TobyBaril about 1 year ago

earlgrey - Earl Grey v5.0.3

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v5.0.2...v5.0.3

- Python
Published by TobyBaril about 1 year ago

earlgrey - 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 https://github.com/TobyBaril/EarlGrey/pull/164

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v5.0.0...v5.0.1

- Python
Published by TobyBaril about 1 year ago

earlgrey - 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 https://github.com/TobyBaril/EarlGrey/pull/146
• Updates for Version 5! by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/150

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.5.0...v5.0.0

- Python
Published by TobyBaril over 1 year ago

earlgrey - 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 https://github.com/TobyBaril/EarlGrey/pull/141

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.4.5...v4.5.0

- Python
Published by TobyBaril over 1 year ago

earlgrey - Earl Grey v4.4.5

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

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.4.4...v4.4.5

- Python
Published by TobyBaril over 1 year ago

earlgrey - Earl Grey v4.4.4

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

- Python
Published by TobyBaril over 1 year ago

earlgrey - Earl Grey v4.4.2

Bug fixes in the divergence calculator scripts.

- Python
Published by TobyBaril over 1 year ago

earlgrey - 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.

- Python
Published by TobyBaril over 1 year ago

earlgrey - 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

- Python
Published by TobyBaril over 1 year ago

earlgrey - Earl Grey v4.3.0

What's Changed

• Patches for Release 4.3.0 by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/114

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.2.4...v4.3.0

- Python
Published by TobyBaril over 1 year ago

earlgrey - Earl Grey v4.2.4

Small patches for stability updates to readme

- Python
Published by TobyBaril almost 2 years ago

earlgrey - v4.2.3

• Patch fixes on new divergence plots

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.2.2...v4.2.3

- Python
Published by TobyBaril almost 2 years ago

earlgrey - Earl Grey v4.2.2

What's Changed

• Version 4.2.0 - Increased Efficiency and Patch Fixes by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/101
• 102 bug when using soft link to genome by @TobyBaril in https://github.com/TobyBaril/EarlGrey/pull/103

Full Changelog: https://github.com/TobyBaril/EarlGrey/compare/v4.1.1...v4.2.2

- Python
Published by TobyBaril almost 2 years ago

earlgrey - Earl Grey v4.2.1

• Small patch fixes and preparations for pandas 3.0

- Python
Published by TobyBaril almost 2 years ago

earlgrey - Earl Grey v4.2.0

• Removed inefficient for loop in final repeat merge step
• updated overlap algorithm to handle nested insertions
• new divergence calculator! This now works on the final merged repeats file and calculated kimura 2-parameter distance
• new plots! new divergence calculator now produces new plots. Same idea - TE landscape, but now with two more plots showing landscapes by TE classifications for more indepth analyses.

- Python
Published by TobyBaril almost 2 years ago

earlgrey - v4.2.0-dev

DEV TESTING

- Python
Published by TobyBaril almost 2 years ago

earlgrey - Earl Grey v4.1.1

• Patches to TEstrainer processing to resolve SSR detection

- Python
Published by TobyBaril almost 2 years ago

earlgrey - Earl Grey v4.1.0

• Updates to the final GFF annotation file to highlight the tool used
• Various updates to the README and documentation

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.8

• Recoded the filtering of overlapping repeats using Dplyr to increase speed and efficiency. Gone are the inefficient for-loops!

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.7

• Small patches to increase the parameters available to users to fine-tine the BEAT process
• It is now possible to specify the number of sequences to be used in TE consensus generation (default 20), the number of flanking bases to be added each time (deafault 1000bp), and the maximum number of BEAT iterations to run (default 10).

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.6

• Patch to add failsafes in case all known repeats are hardmasked by the initial RepeatMasker run, which previously caused TEstrainer to fail.
• A warning is now pushed to the log in case this behaviour is not expected by the user.
• Beware of using small subsets for testing, it is unlikely RepeatModeler2 can find repetitive DNA in tiny portions of test sets!

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.5

Patch creation of dictionary.

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.4

Small patch in intitial genome preparation. No change in analysis outputs from previous version.

- Python
Published by TobyBaril about 2 years ago

earlgrey - 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

- Python
Published by TobyBaril about 2 years ago

earlgrey - Earl Grey v4.0.2

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

- Python
Published by TobyBaril about 2 years ago

earlgrey - 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.

- Python
Published by TobyBaril about 2 years ago

earlgrey - 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!

- Python
Published by TobyBaril over 2 years ago

earlgrey - 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.

- Python
Published by TobyBaril over 2 years ago

earlgrey - 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.

- Python
Published by TobyBaril over 2 years ago

earlgrey - 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 TEstrainerforearlGrey.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

- Python
Published by TobyBaril over 2 years ago

earlgrey - 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

- Python
Published by TobyBaril over 2 years ago

earlgrey - 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.

- Python
Published by TobyBaril over 2 years ago

earlgrey - Earl Grey v2.4

- Python
Published by TobyBaril over 2 years ago

earlgrey - v2.3

• Bug fixes
• Documentation updates

- Python
Published by TobyBaril almost 3 years ago

earlgrey - Earl Grey v2.2

• Bug fixes
• Updates to retain compatibility with the latest versions of RepeatModeler (2.0.4) and RepeatMasker (4.1.4)
• Significant updates to the docker container, along with the publication of a docker image preconfigured with Dfam 3.7 curated elements
• Small corrections to documentation

- Python
Published by TobyBaril almost 3 years ago

earlgrey - Earl Grey v2.1

• Bug fixes and further improvements to the new "Blast, Extract, Extend" process
• Updated to work with RepeatMasker 4.1.4 and RepeatModeler 2.0.4
• Docker contained updated to include new RMBlast 2.13.0
• Documentation updated to reference Dfam 3.7 and RMBlast 2.13.0

- Python
Published by TobyBaril about 3 years ago

earlgrey - Earl Grey v2.0

Updated Earl Grey Release

Updates: - Initial RepeatMasker step is now optional, with default being no RepeatMasker run. This provides more information for the do novo RepeatModeler run to generate better TE consensus models for a species of interest. If required, an initial RepeatMasker step can still be run using the -r flag, specifying the library required. - New BLAST, Extract, Align, Trim process. Completely overhauled BEAT process to extend TE consensus sequences to their boundaries. No fuzzy ends are now observed, and consensus sequences are only extended if required, not once ends are reached. - Clustering is now optional, with default being no clustering. TE library sequences can be clustered to reduce TE library redundancy. However, this can have adverse effects on the identification of subfamilies and of independently-transposing chimeric TEs, where members of the chimeric TE will be labelled as subregions of the larger TE, rather than a separate unit. - New TE classification step. This is still homology based, but is now incorporated into the BEAT process above. This makes use of RepeatClassifier from RepeatModeler2 to classify newly-identified TEs after extension.

- Python
Published by TobyBaril about 3 years ago

earlgrey - Earl Grey v1.3

New script to resolve overlapping repeats to cut analysis time

- Python
Published by TobyBaril over 3 years ago

earlgrey - Earl Grey v1.2

For those that cannot install RepeatModeler and RepeatMasker on their systems, we now provide a Docker container (with instructions) that will enable Earl Grey to run within a virtual environment.

- Python
Published by TobyBaril over 4 years ago

earlgrey - Earl Grey v1.1

Added improved error catch for RepeatModeler failure when running on genomes of particular sizes

- Python
Published by TobyBaril over 4 years ago

earlgrey - Earl Grey

First Release of Earl Grey: A fully automated combined library-based and de novo TE annotation pipeline, integrating a BLAST, Extract, Extend process and generating informative summary figures for any input genome.

- Python
Published by TobyBaril over 4 years ago