7 This toll will extract library of repeats based on RepeatExplorer2 analysis. Library is available as fasta file. Tool also filter out all the contig parts which has read depth and length below threshold. Parts of contigs with read depth below threshold are hardmasker. Contigs with full hardmasking are removed completelly
21 Internally annotation is performed using RepeatMasker search. Output from RepeatMasker is parsed to remove duplicated and overlaping annotations, Conflicts in annotations are resolved using hierarchical classification of repeats provided in custom database.
