Toolkit for Population Genetic Statistics from Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments
GPL-3.0 License
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This is the first release since the grenedalf manuscript came out 🥳
grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
Bioinformatics, 2024. doi:10.1093/bioinformatics/btae508
Published by lczech 3 months ago
This release adds some features related to position masking. Furthermore, it renames a few options for consistency: Options that ended in -file
are now more concisely named.
--make-gapless
option #26-file
option names for clarityPublished by lczech 4 months ago
Published by lczech 4 months ago
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data, #21Published by lczech 4 months ago
This release fixes the wrong computation of FST window averages that slipped our attention in grenedalf v0.4.0, and adds tests to avoid these types of accidents in the future. Other than that, please see v0.4.0 for the major updates of this version compared to the previous v0.3.0.
Published by lczech 5 months ago
This release contains a major redesign of the data filtering approach, which now allows to properly compute window averages of the statistics, and improves the behavior of the SNP queue window approach. It furthermore contains several refinements of the statistics, and offers more options than before. Some options have been renamed to fit with the new functionality.
ATTENTION: We accidentally introduced a bug in the window averaging of FST that slipped our attention. We are currently working on a fix, which will be released asap. Please use fst --window-average-policy absolute-sum
in the meantime only.
Published by lczech about 1 year ago
Published by lczech over 1 year ago
This release accompanies our preprint
grenedalf: population genetic statistics for the next generation of pool sequencing.
Lucas Czech, Jeffrey P. Spence, Moisés Expósito-Alonso.
arXiv, 2023. arXiv:2306.11622
grenedalf is still very much in development, and a lot of things will further change, such as the command structure and option names. We are lacking documentation, and there are some known smaller issues. That will all be fixed in the near future. However, since its initial pre-release more than a year ago, a lot has changed and improved. We hence consider it workable enough. But still, please report any issues that you are having - grateful for your feedback!
Stay tuned for more!
A lot has happened since v0.1.0, but here is a very broad summary:
Published by lczech over 2 years ago
This (pre-)release is meant for those who have (thankfully) been working with grenedalf already, as a point of reference.
It is not to be considered stable - things WILL change!