FIGURE 4.

Pipeline used for satDNA analysis in this study. A typical clustering of raw reads with RepeatExplorer is performed to search for a consensus satDNA sequence. After that, this consensus sequence is used as reference (dotted arrow) to collect monomers directly from the reads using a series of custom python scripts. The isolated monomers are then analyzed for different features, such as intragenomic diversity and nucleotide analyses. Also, a strategy combining PCR, cloning and Sanger sequencing might be performed to isolate monomers if NGS reads are not available. Finally, a global alignment is then performed to construct minimum-spanning-trees.