Fig. 5

TT-Mars Workflow. a Assembly contigs are aligned to the reference, and the shorter of two overlapping contigs are trimmed to generate a unique mapping. Regions on the reference that are not covered by contigs are excluded. b The alignment is used to construct an orthology map at specific intervals (e.g., every 20 bases). c For an SV, called at an interval [s, e] on the reference, TT-Mars searches the orthology map for matches outside the interval that most closely reflects the length of the SV. In this example, the interval [a, b] immediately flanking a deletion SV maps to an interval on the assembly that does not reflect the SV, but a wider search in the orthology map shows that [c, b] spans a deletion in the assembly. d–g Validation details by a deletion example. d TT-Mars takes the candidate call with w flanking bases on both sides. The interval on the reference is compared with an interval on the assembly (e) before and after the SV operation. In f and g, the deletion operation removes the corresponding sequence on the reference and is validated if the modified reference is more similar to the assembly than the original