Nucleic acid rearrangement and integration analysis

A method of identifying an integration breakpoint position in a genome of an organism comprising a pathogen integration, the method comprising:

• (a) obtaining a plurality of paired-end sequencing reads for cell-free nucleic acid molecules from a biological sample of the organism;
• (b) performing a first alignment of the plurality of paired end sequencing reads, with a first alignment algorithm, wherein the first alignment identifies one or more Type A fragments comprising (i) a first sequence read of a read pair that aligns to a reference genome of the organism, and (ii) a second sequence read of the read pair that aligns to a reference genome of the pathogen;
• (c) identifying one or more candidate integration regions in the reference genome of the organism, wherein a candidate integration region is identified as being within 500 bases of where one of the first sequence reads of a Type A fragment aligns;
• (d) performing a second alignment of a subset of the plurality of paired end sequencing reads against the one or more candidate integration regions with a second alignment algorithm, wherein the second alignment identifies one or more Type B fragments comprising (i) a first sequence read of a read pair that aligns to the reference genome of the organism or the reference genome of the pathogen, and (ii) a second sequence read comprising a first portion that aligns to one of the one or more candidate integration regions and a second portion that aligns to the reference genome of the pathogen;
• and
• (e) identifying the integration breakpoint position at a junction formed by the first portion and the second portion of the second sequence read of one of the one or more Type B fragments.