https://github.com/lczech/pool-seq-pop-gen-stats - 2024-07-23

See the "Assets" list below for the PDF.

Notable changes:

• Fix the typography of F_ST to use italics F. Thanks to Martin Kapun (@capoony) for the hint!

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Published by lczech over 1 year ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2024-06-07

See the "Assets" list below for the PDF.

Notable changes:

• Add information on window averaging to obtain per-base-pair estimates

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Published by lczech over 1 year ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2024-05-30

Minor update. See the "Assets" list below for the PDF.

Notable changes:

• Rename all occurrences of "coverage" to "read depth", as that is the more appropriate and less ambiguous term

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Published by lczech over 1 year ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2023-09-12

This release accompanies our submission of the grenedalf preprint to Bioinformatics. See the "Assets" list below for the PDF.

Notable changes:

• Fix accidental extra harmonic term in the equations for Watterson's Theta (equations 15-16 in this document).
• Fix surplus plus sign in the Karlsson Fst estimator equation (equation 51 in this document), as well as a renaming of variables u and v in that section to p and q for better readability.

Both fixes only affected the document, and not our implementation, where the equations were correct.

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Published by lczech over 2 years ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2023-08-02

Minor update. See the "Assets" list below for the PDF.

Notable changes:

• Add some intuition for the Fst Bessel's correction. Thanks to Jennifer McIntyre for inquiring this!

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Published by lczech over 2 years ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2023-06-19

This release accompanies the grenedalf 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

See the "Assets" list below for the PDF.

Notable changes:

• General improvements in consistency of notation and level of detail
• Add section "Conclusion and Comprehensive Approach" describing our latest findings about Tajima's D
• Remove figure "Examination of the effect of the bugs in the computation of Tajima's D in PoPoolation"

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Published by lczech over 2 years ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2023-04-12

This version of the document is the basis for the independent implementation of the equations in Python that we used to verify grenedalf. We provide this version here as a reference for the equation numbers in that Python implementation. We further intend to use that code as a basis for providing a set of test files to be used to check other implementations. See the link above for details.

See the "Assets" list below for the PDF.

Notable changes:

• Add figure "Examination of the effect of the bugs in the computation of Tajima's D in PoPoolation"
• Add section "Unbiased estimates of heterozygosity in the presence of sequencing error"

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Published by lczech over 2 years ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2022-06-05

This release accompanies our submission of the below preprint to eLife Tools and Resources. See the "Assets" list below for the PDF.

Notable changes:

• Overall consistency and readability improvements
• Fix the correction term for Theta Watterson
• Add section "Comparison of the Estimators and their Biases" using simulation to show the biases of FST estimators

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Published by lczech over 3 years ago

https://github.com/lczech/pool-seq-pop-gen-stats - 2022-02-02

First version of the document, which was also included in our preprint:

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing. Lucas Czech, Yunru Peng, Jeffrey P. Spence, Patricia L.M. Lang, Tatiana Bellagio, Julia Hildebrandt, Katrin Fritschi, Rebecca Schwab, Beth A. Rowan, GrENE-net consortium, Detlef Weigel, J.F. Scheepens, François Vasseur, Moises Exposito-Alonso. bioRxiv, 2022.02.02.477408; doi:10.1101/2022.02.02.477408

See the "Assets" list below for the PDF.

- TeX
Published by lczech over 3 years ago