Figure 6

Pipeline for satDNA analysis.

The mining steps start with raw reads and a typical clustering with RepeatExplorer. This yields linear, spherical or ring-shaped clusters, the two latter types most likely being satDNAs. Each of these clusters is then split into monomers to search for a consensus satDNA sequence. The assembled sequences and those showing homology with those included in Repbase and a custom database, were used to filter a new set of raw reads before performing a new RepeatExplorer run. Several clustering and filtering steps were performed until no new satDNA appeared. This increased the number of reads analyzed by Repeat Explorer without greatly increasing computing requirements. The satDNA collection obtained is then analyzed for different features such as homology between different consensus sequences and their intragenomic diversity and a repeat landscape is built.