Additional file 2 of VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites

In silico dataset and accuracy assessment results. The excel table reports the list of all IS (in rows) and the corresponding output returned by the different tools (divided by colors in the following order: VISPA, VISPA2, MAVRIC, SEQMAP, QUICKMAP). For each read (identified by its “ID” in column “header”), we reported the source genomic coordinates (in columns chromosome “chr”, integration point “locus”, and orientation “strand”), the source of annotation as described in VISPA [22] and the nucleotide sequence. Then we reported the output of IS for each tool: the first set of columns report the returned IS genomic coordinates (columns “header”, “chr”, “locus” and “strand”), whereas the other columns label each IS for statistical assessment as true positive (TP), false positive (FP), and false negative (FN) based on the genomic distance (“IS distance”) from the ground truth. Precision and recall are then derived by the columns of TP, FP, and FN. (XLSX 233 kb)