HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads

BMC Bioinformatics

Table 3 QAN50 on the real Ashkenazim dataset, Chromosome 1

Avg.	HapCHAT	HapCol	WhatsHap	WhatsHap	HapCUT2	ReFHap	ProbHap	FastHare
Cov.			cov. 15x	cov. 20x
25	79452	76856	79515	79515	78192	48097	45492	45445
30	80662	80150	80426	80426	80150	52713	50806	49308
35	81842	81464	81757	81757	81464	54182	-	51766
40	83968	82758	83802	83802	83263	57589	-	55014
45	87267	86001	87267	87267	86001	59161	-	57008
50	89669	89738	89858	89858	89306	60380	-	59447
55	91434	91434	91224	91224	90718	62652	-	59582
60	94913	92938	95818	95818	92565	64710	-	62655

For each dataset, its row identified by its average coverage (Avg. Cov.). We report the results obtained by running the tools with maximum coverage 30 × for HapCHAT, 25 × for HapCol, 15 × and 20 × for WhatsHap. No maximum coverage was set for HapCUT2, ReFHap, ProbHap, and FastHare. The best result (highest value) for each dataset is boldfaced

ISSN: 1471-2105