Supplementary files for Chapter 2 of my master's dissertation "Jellyfish repeatomes uncover hidden satellite diversity and provide insights into the C-value enigma"

The files and directories included in this folder include the following:

/RepeatExplorer/ directory including datasets resulting from RE2 pipeline
and the scripts used to process them and carry on
statistics.

/RepeatExplorer/AssemblyAnalysis.py Python script used to manipulate files resulting from
  repeatmasker repeat annotation in assemblies,   to identify clusters after clusterscan,   and to classify them into proximal or distal to gaps and ends.

/RepeatExplorer/ScyphoSat_table table containing all information regarding satellite monomers obtained with RE2, including manual curation
  information, classification and sequence information.

/RepeatExplorer/assemblySat_plots.py Python script to plot the distribution of intragenomic divergence of satellites in assemblies and reads.

/RepeatExplorer/Genus_ComparisonStats.py Python script to compare satDNA features distribution in   samples of the same genus.

/RepeatExplorer/SampleStatistics.py Python script to compare satDNA features across all
  species and samples.

/RepeatExplorer/duplicateMonomer.py Python script to duplicate and rename satDNA monomers.

/RepeatExplorer/filterBlastn.py Python script to classify satDNA blast hits as variants,   families and superfamilies.

/dnaPipeTE/ directory including datasets resulting from dnaPipeTE and the scripts used to process them and carry on statistics

/dnaPipeTE/SupplementaryTableS2extended general repetitive content information including detailed abundance information about all TE Superfamilies

/dnaPipeTE/dnaPipeTE_spearmanr.R R script used for statistical analysis between genome
  size and dnaPipeTE results

/dnaPipeTE/filter_RTcompleteness.py Python script used for filtering protein domains with
  coverage below certain threshold