Fig. 1

Utilizing long insert mate pair reads to localize retrovirus integrations. Reference human genome is shown as a blue line with the location of a novel inserted retrovirus in a patient sequence, in orange, indicated by a dotted vertical orange line. Long insert mate pair reads are linked by gray dotted lines, with the read derived from the new retrovirus, which will not map, shown in orange, it’s mate that maps to the human reference genome shown in blue. Depending on the length of the retrovirus, which typically is 6–10 kbp, some mate pairs may span the entire inserted virus and hence both mate pairs will originate from the host (light blue), resulting in mate pairs that map at a distance shorter than the expected insert distribution of 5–12 kbp. A retrovirus insertion site is suggested by a combination of several features of mate pair mapping including short insert intervals and discordant or broken mate pairs. The insert length and depth of mapped reads are key signals in our retrovirus insertion pipeline (see Additional file 1: Supplementary Methods; Figure S1). The unmapped reads (orange in the figure) from discordant mate pairs at each called insertion site are assembled and used to determine the sequence of a candidate retrovirus