https://github.com/k8hertweck/flypopgenomics

transposon and LD analysis for replicated experimental evolution fruit fly populations
https://github.com/k8hertweck/flypopgenomics

drosophila genomics ldx popoolation transposable-elements

Last synced: about 1 month ago
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transposon and LD analysis for replicated experimental evolution fruit fly populations

• Host: GitHub
• URL: https://github.com/k8hertweck/flypopgenomics
• Owner: k8hertweck
• Created: 2012-12-11T15:08:56.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2017-07-20T17:32:22.000Z (over 7 years ago)
• Last Synced: 2023-04-04T08:51:58.200Z (over 1 year ago)
• Topics: drosophila, genomics, ldx, popoolation, transposable-elements
• Language: R
• Homepage:
• Size: 3.75 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# fly population genomics scripts

Data available from NCBI SRA BioProject: PRJNA285429

Associated publication: [Graves Jr, J.L., Hertweck, K.L., Phillips, M.A., Han, M.V., Cabral, L.G., Barter, T.T., Greer, L.F., Burke, M.K., Mueller, L.D. and Rose, M.R., 2017. Genomics of Parallel Experimental Evolution in Drosophila. Molecular biology and evolution, 34(4), pp.831-842.](https://academic.oup.com/mbe/article/2897202)

## Linkage disequilibrium (LD) using [LDx](https://sourceforge.net/projects/ldx/)

* implements scripts to run LDx using slurm

## Transposable elements using [popoolationTE](https://sourceforge.net/p/popoolationte/wiki/Main/)

* creates necessary files and runs popoolationTE to identify de novo TE insertions from pooled population sequencing