Table 1.

Overview of the gold standard datasets

	D1	D2	D3	D4	D5
Technology	Whole genome sequencing	T cell receptor sequencing	T cell receptor sequencing	Viral sequencing	Viral sequencing
Heterogeneity	Low	High	High	High	High
Technique	Simulated	UMI-based error-free reads	Simulated	UMI-based error-free reads	Haplotype-based error-free reads
Number of samples	12	8	6	1	11