Offers an approach for an automatized gathering of features from complex repeat sequences. JuctionViewer is a standalone software which was initially developed for discovering, filtering, and visualizing relevant features of the sequenced DNA of maize centromeres. It merges various types of annotations and generates graphical representations of sequences. The application also can be used for annotating repeat-rich regions in other organisms or displaying of sequence coverage data.
A method that jointly calls all centromeres in a genome-wide Hi-C contact map. The key idea is that a joint optimization can effectively exploit the clustering of centromeres in 3D. Centurion works well even with very limited sequencing depth Hi-C libraries generated from pooled samples, making it a practical as well as powerful tool to use on single microorganisms and metagenomic mixtures.