Author response table 3. Statistics for the different approaches used to assemble the var transcripts.

Var assembly approaches were applied to malaria patient ex vivo samples (n=32) from (Wichers et al., 2021) and statistics determined. Given are the total number of assembled var transcripts longer than 500 nt containing at least one significantly annotated var domain, the maximum length of the longest assembled var transcript in nucleotides and the N50 value, respectively. The N50 is defined as the sequence length of the shortest var contig, with all var contigs greater than or equal to this length together accounting for 50% of the total length of concatenated var transcript assemblies. Misassemblies represents the number of misassemblies for each approach. *Number of misassemblies were not determined for the domain approach due to its poor performance in other metrics.

	Number of contigs≥ 500nts	Maximum length (nt)	Average contig length (nt)	N50	Number of misassemblies
Original approach	6,441	10,412	1,621	2,302	336
Domain approach	4,691	5,003	954	1,088	NA*
Whole transcript approach	3,011	12,586	2,771	5,381	2