Fig. 1

Figure describing the main steps of retrotranscription, amplification of RNA and sequencing (a) and the viral reads’ filtering method (b). This method is divided in different parts. The first part obtains all reads in Fasta format after different types of filtration steps. The second step aims at selecting only the viral part in each read using a similarity-based approach. Finally, the last step is to perform assembly using different algorithms with targeted sequences. HTS high throughput sequencing; cDNA complementary DNA; ssDNA single strand DNA