R script to annotate sequences (e.g. SatDNA) in chromosome-level assemblies.
The pipeline needs an annotation step made in Geneious. The similarity we recommend is around 75-80% for SatDNA families. You must to export a .gff file with only the annotations. Each satellite DNA family must be annotated with its corresponding name in the Geneious annotation property "Type." Then you only need to run this script in R, providing also a .txt file containing chromosome names and the length of each one for plotting (Not necessary for CHRISMAPP_V2).
A revised version of this script has been introduced, incorporating the following enhancements:
-Elimination of the requirement for a .txt file containing chromosome names and sizes. Instead, this updated script retrieves chromosome length data directly from the Geneious .gff file.
-Integration of a feature enabling the generation of a new PDF file that consolidates all individual annotation graphs.
Rico-Porras, J.M.; Mora, P.; Palomeque, T.; Montiel, E.E.; Cabral-de-Mello, D.C.; Lorite, P. Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae). Genes 2024, 15, 395. https://doi.org/10.3390/genes15040395