Table 1 Overview of features of the mobile element detection tools evaluated in this study.

Tool	Type of reads^a	Input	Output	ES^b	Year, Reference	Source
ERVcaller	Discordant pairs + Split or clipped reads	FASTQ or BAM	VCF file	Yes	2019, ²¹	https://github.com/xunchen85/ERVcaller
MELT	Discordant pairs + Split or clipped reads	BAM (aligned with BWA) or CRAM	VCF file	Yes	2016, ^14,16	https://melt.igs.umaryland.edu
Mobster	Discordant pairs + Split or clipped reads	BAM	Text file	Yes	2014, ¹⁷	https://github.com/jyhehir/mobster
SCRAMble	Split or clipped reads	BAM	VCF file	Yes	2020, ¹³	https://github.com/GeneDx/SCRAMble
TEMP2	Discordant pairs + Split or clipped reads	FASTQ or BAM	BED file	No	2021, ²²	https://github.com/weng-lab/TEMP2
xTea	Discordant pairs + Split or clipped reads	BAM or CRAM	VCF file	Yes	2021, ²³	https://github.com/parklab/xTea

^aType of reads used by the algorithm to detect MEIs in sequencing data.
^bThe ES column specifies whether the tool can be used for ES data as described by the author.
Abbreviations: ES, exome sequencing; MEI, mobile element insertion.

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