Table 1.

Runtimes of the compared methods

Chain	(Pre)alignments			Probabilistic treatment
	MiXCR	Partis	IGoR/RepgenHMM	MiXCR	Partis	RepgenHMM	IGoR
TRA 100 bp	2 × 10−4	NA	0.3	NA	NA	10−2	10−4
TRB 60 bp	3 × 10−4	NA	0.1	NA	NA	1	0.1
IGH 130 bp	10−3	10−2	0.2	NA	5 × 10−2	>1	0.2

Times for alignments are in seconds per sequence. In the probabilistic treatment, times are in seconds per sequence per iteration for Partis, and in seconds per sequence per EM iteration for IGoR and repgenHMM. MiXCR only performs alignments and does not include a probabilistic treatment. Partis only handles BCRs. IGoR and repgenHMM share the same code for pre-alignment. NA not applicable