Scripts and files associated with the gene based definition of Nigon units, identification of germline restricted regions and chromosomal assembly of O. tipulae manuscript

---

Prerequisites can be installed via:

conda create -n otipu -c r -c conda-forge r-base r-tidyverse r-reshape2 r-scales r-gtools r-ggpubr r-cluster r-tsne
conda activate otipu

After cloning the repository, R scripts can executed from the master directory. Figures can be found under report/figure while analysis results will be generated under analysis.

git clone https://github.com/tolkit/otipu_chrom_assem.git
cd otipu_chrom_assem
Rscript scripts/nigon_definition.R

To regenerate the circos plot, circos must have been installed.

cd otipu_chrom_assem/analyses/circos
circos -conf etc/Oscheius_tipulae_3.3_all_chromosomes_Pif.circos.conf
circos -conf etc/Oscheius_tipulae_3.3_telomeres.conf