Table 2.

Tools for TE Insertion Genotyping

Read type	Method	Genotyping strategy	Graph alignment
Short reads	MELT (Gardner et al., 2017)	Maximum likelihood	No
Short reads	GHSTDEL (Chu et al., 2014)	Machine learning	No
Short reads	TypeTE (Goubert et al., 2020)	Maximum likelihood	No
Short reads	xTea (https://github.com/parklab/xTea)	Machine learning	Yes
Short reads	Paragraph (Chen et al., 2019)	Maximum likelihood	Yes
Short reads	GraphTyper2 (Eggertsson et al., 2019)	Maximum likelihood	Yes
Short reads	vg toolkit (Hickey et al., 2020)	Heuristic	Yes
Long reads	SVJedi (Lecompte et al., 2019)	Maximum likelihood	No
Long reads (phasing)	NanoSV (Cretu Stancu et al., 2017)	Heuristic	No