Table 1.

Features of user-facing tools for SatDNA reconstruction

Tool	Reads	Contigs	De novo	HORs
Alpha-CENTAURI	Yes	No	No	Yes
HiCAT	No	Yes	No	Yes
HORmon	No	Yes	No	Yes
NTRprism	No	Yes	Yes	Yes
SRF (this work)	Yes	Yes	Yes	Yes
TAREAN	Yes	No	Yes	No

“Reads”: whether the tool works with unassembled reads. “Contigs”: whether the tool works with high-quality contigs. “De novo”: whether the tool works without known monomer sequence as input. “HORs”: whether the tool can identify high-order repeats (HORs). References to these tools can be found in the Introduction section.