Table 1.

Tools for TE Insertion Detection

Sequence read type	Method	TE sequence library	TE-specific annotation
PE short reads	Tea (Lee et al., 2012)	Yes	Yes
PE short reads	MELT (Gardner et al., 2017)	Yes	Yes
PE short reads	Mobster (Thung et al., 2014)	Yes	Yes
PE short reads	RetroSeq (Keane et al., 2013)	Yes	Yes
PE short reads	TraFiC (Tubio et al., 2014)	Yes	Yes
PE short reads	TEMP (Zhuang et al., 2014)	Yes	Yes
PE short reads	T-lex3 (Bogaerts-Márquez et al., 2019)	Yes	Yes
PE short reads	Tangram (Wu et al., 2014)	Yes	Yes
PE short reads	ITIS (Jiang, Chen, Huang, Liu, & Verdier, 2015)	Yes	Yes
Long reads	Sniffles (Sedlazeck et al., 2018)	No	No
Long reads	SVIM (Heller & Vingron, 2019)	No	No
Long reads	pbsv (https://github.com/PacificBiosciences/pbsv)	No	No
Long reads	PBHoney (English, Salerno, & Reid, 2014)	No	No
Long reads	PALMER (Zhou et al., 2019)	No	Yes
Multiple platforms	xTea (https://github.com/parklab/xTea)	Yes	Yes
PE short reads	DD_DETECTION (Kroon et al., 2016)	No	Yes
PE short reads	TranSurVeyor (Rajaby & Sung, 2018)	No	Yes