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

BMC Bioinformatics

Table 4 A comparison of scaffolded assemblies after Hi-C analysis, based on HapSolo and purge_dups primary assemblies

Species^a	Chardonnay		Mosquito		Thorny Skate
Assembly type	HapSolo +HC^b	purge_dups	HapSolo +HC	purge_dups	HapSolo +HC^e	purge_dups
# of Scaffolds	2403	294	611	635	10,009	1534
% of Genome in k largest scaffolds^c	88.0%	58.5%	85.7%	83.7%	106.3%	86.8%
% of Genome in scaffolds > 10M^d	97.7%	67.4%	94.1%	92.7%	105.6%	86.0%
Scaffold assembly size (Mb)	540.1	470.4	200.4	200.3	3039.3	2251.4
Largest scaffold (Mb)	36.5	24.9	95.0	74.1	250.5	184.1
Scaffold N50 (Mb)	20.7	12.7	41.6	51.2	69.8	61.7
Scaffold L50	11	15	2	2	13	11

^aData for HapSolo are based on BLAT alignments for Chardonnay and mosquito, and minimap2 alignments for thorny skate
^bResults in the +HC columns are based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
^cPercentage of genome in the largest k scaffolds, where k is equal to the number of chromosomes expected for each species. Percentages are normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for Chardonnay, mosquito and thorny skate respectively
^dPercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
^eResults for HapSolo were generated using minimap2

ISSN: 1471-2105