HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

BMC Bioinformatics

Table 3 Scaffolded assembly statistics after Hi-C analysis on HapSolo assemblies, for three primary assemblies for each of three species

Species	Chardonnay			Mosquito			Thorny Skate^f
Assembly type	No HapSolo^a	HapSolo −HC^b	HapSolo +HC^c	No HapSolo	HapSolo −HC	HapSolo +HC	No HapSolo	HapSolo −HC	HapSolo +HC
# of Scaffolds	1332	2748	2403	1211	603	611	14,238	12,269	10,009
% of Genome in k largest scaffolds^d,e	52.0%	89.0%	84.0%	61.9%	68.3%	85.7%	31.5%	104.7%	106.3%
% of Genome in Scaffolds > 10Mb^e	44.0%	94.0%	94.0%	93.5%	94.7%	94.1%	40.4%	103.3%	105.5%
Scaffold assembly size (Mb)	656.1	570.4	540.1	212.5	200.8	200.3	3240	3158	3039
Largest scaffold (Mb)	19.1	32.6	36.5	43.6	53.0	95.0	170.0	208.4	250.5
Scaffold N50 (Mb)	7.2	23.5	20.7	37.9	41.5	41.6	62.1	65.5	69.8
Scaffold L50	28	11	11	3	3	2	16	35	13

^aResults in this column were based on the primary assembly without application of HapSolo
^bResults in this column were based on application of HapSolo without hill climbing (−HC) and default parameters of ID, Q and QR
^cResults in this column were based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
^dPercentage of genome in the largest k scaffolds, where k is equal to the number of chromosomes expected for each species
^ePercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
^fResults for HapSolo were generated using minimap2

ISSN: 1471-2105