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 correspond to "Supplementary file S1" of the dissertation and include the following:
| directory/file | description |
|---|---|
| /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 |
| /dnaPipeTE/RenameContigs.py | Python script to rename dnaPipeTE unclassified contigs using TEsorter output |