Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

Table 1 Major features that distinguish the original McClintock version reported in Nelson et al. [15] and the McClintock 2 system reported in the current study

	Nelson et al. [15]	McClintock 2
McClintock implementation	Bash	Python
Workflow management	N.A.	Snakemake
Dependency installation	Manual	Conda (automated)
# Component methods	6	12 (with extensibility)
Read trimming and QC	N.A.	trimgalore module
TE copy number estimation	N.A.	coverage module
Output format	.BED	.VCF and .BED
Summary report	.CSV	.CSV and .HTML (interactive)
Reproducible simulation system	N.A.	Built-in (with documentation)

ISSN: 1759-8753