Genome data and resources on the recombination landscape and population history of the harlequin fly

This dataset contains phased vcf files of Chironomus riparius, ouput files of RepeatMasker, MELT, RepeatOBserver, MSMC2, iSMC and bedtools, such as supporting files. 

For further details also check the GitHub page: https://github.com/lpettrich/Crip_Recombination_PopHistory_Cla_2024

• phased-vcfs: Artificially phased vcf-files of five populations with four individuals each. Needed to generate multihetsep files. Input files for iSMC.
  
  • Hesse in Germany =  MG
  • Rhône-Alpes in France = MF
  • Lorraine in France = NMF
  • Piemont in Italy = SI
  • Andalusia in Spain = SS
• multihetsep-files: Created with msmc-tools. Input files for MSMC2. 
• RepeatMasker: Raw output of RepeatMasker run. Summary file and file with filtered Cla-element (a transposable element) included.
  
• MELT: MELT ouput with added info on population and numbered insertions reflecting all 441 detected Cla insertions.
  
• RepeatOBserver: Summary files on centromere predictions based on histograms and Shannon Diversity from RepeatOBserver. Genome-wise Shannon Diversity per chromosome included.
  
• MSMC2: Raw ouput of combined cross-coalescence and mean values if MSMC2 per populations.
  
• iSMC: Recombination rate rho in 10 kb windows and 100 kb windows along the genome.
  
• bedtools closest ismc 10 kb: Bedtools closest analysis of the distance of the next Cla-element to the recombination rate rho in 10 kb windows.
  
• bedtools closest ismc 100 kb: Bedtools closest analysis of the distance of the next Cla-element to the recombination rate rho in 100 kb windows.
• input-files figures: Supporting files needed to create figures.