Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula

Table 1 Number and characteristics of contigs and scaffolds for each of the five assemblies

	PacBio (Pb)	PacBio BioNano (PbBn)	PacBio Dovetail (PbDt)	PacBio BioNano Dovetail (PbBnDt)	PacBio Dovetail BioNano (PbDtBn)
Assembly software	FALCON	FALCON Irys	FALCON HiRise	FALCON Irys HiRise	FALCON HiRise Irys
Contigs	1, 073	1, 073	1, 121	1, 125	1, 121
Contig Length	396,973,838	396,973,942	396,973,838	396,973,942	396,973,934
Contig N50^a	3,768,504	3,768,512	3,768,504	3,768,512	3,768,504
Scaffolds	1, 073	993	1, 005	965	942
Scaffold Length	396,973,838	401,421,527	396,985,438	401,429,527	399,955,467
Maximum Scaffold Length	13,488,151	22,885,216	19,275,758	12,137,306	12,557,854
Scaffold N50^a	3,768,504	6,819,834	6,895,511	12,137,306	12,557,854

^aN50 s were also adjusted to use an assembly length of 400 Mb for all assemblies in order to facilitate comparisons across assemblies. Scaffold and contig N50 s adjusted for a 400 Mb assembly size were identical to unadjusted N50 s shown above, except for the PbDt scaffold N50 for which the adjusted N50 was 6,348,449 nt

ISSN: 1471-2164