MEIGA (Mobile Element Integration Genome Analyser)

MEIGA (Mobile Element Integration Genome Analyser) is a method for comprehensively characterizing the patterns of somatic retrotransposition in long-read sequencing data. MEIGA is capable of detecting not only insertions mediated by retrotranspons but also other types of rearreagements mediated by their activity. These include Deletions (DEL), duplications (DUP), inversions (INV), translocations (TRA) or other complex rearrangements mediated by the integration of L1 and other mobile elements. Retrotransposition events can be further classified based on the type of sequence that has been retrotransposed. These events can be categorized as follows:

Solo insertons, which are full or partial sequences of L1, Alu and SVA.
L1 partnered transductions, in which a L1 sequence along with a piece of sequence downstream are retrotransposed.
L1 orphan transductions, in which only the unique sequence downstream of an active L1 is retrotransposed without the cognate L1.
Processed pseudogenes, which include events where cellular mRNA is retrotransposed using L1 machinery.
Solitary poly(A) tracts from severely truncated retrotranspositions.