Figure 2.

The analysis pipeline of RD-based methods consists of four main stages. The first two stages consist of preparatory operations aimed at generating the RD signal. Sequencing produces artifacts that affect the alignment and consequently the RD signal. Different filtering operators can be applied to reduce these errors. Moreover, alignments must be post-processed to remove those of low quality and to resolve ambiguities. Finally, the RD signal is calculated taking into account the bias related with the GC-content.