HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

BMC Bioinformatics

Table 2 Assessment of HaplotypeTools and WhatsHap on simulated paired reads (100nt or 10 kb) from 100/kb, 10/kb and 1/kb heterozygosity levels

Tool	Param	Het. (/Kb)	Read Length (nt, paired)	Hap n	Genome coverage (%)	Hap N_max	Hap N₅₀	SE	SER	QAN50	Time
HT	default	100	100	95,532	83.2	2867	342	6248	0.0031	248	27 m41 s
HT	default	10	100	33,962	12.0	620	109	25	0.0002	N.D	32 m33 s
HT	-m 2	10	100	34,423	12.1	620	109	32	0.0003	N.D	30 m14 s
HT	default	1	100	728	0.2	211	66	0	0.0000	N.D	32 m59 s
HT	-m 2	1	100	875	0.2	211	64	1	0.0005	N.D	29 m42 s
HT	default	100	10,000	61,536	73.3	6455	528	4242	0.0024	267	31 m13 s
HT	-m 2	100	10,000	56,825	80.5	6455	605	4185	0.0022	353	27 m53 s
HT	-m 2 -r 100 kb	100	10,000	56,903	80.3	11,694	612	4185	0.0022	350	23 m13 s
HT	default	10	10,000	5,965	78.6	9995	6480	35	0.0002	4254	29 m14 s
HT	default	1	10,000	2,492	57.7	9946	7774	0	0.0000	5888	27 m
WH	default	100	100	366	95.1	8,43,884	3,08,400	35,461	0.0163	9,91,296	95 m56 s
WH	default	10	100	2,496	92.7	74,839	17,864	1570	0.0070	19,555	14 m29 s
WH	default	1	100	6,540	12.1	3932	578	235	0.0192	N.D	43 s
WH	default	100	10,000	128	89.1	8,43,900	3,60,273	29,373	0.0144	9,36,966	23 m27 s
WH	default	10	10,000	130	90.0	8,74,030	4,00,757	347	0.0016	4,64,693	3 m11 s
WH	default	1	10,000	196	88.0	7,52,451	2,03,122	18	0.0009	97,221	24 s

Haplotype (Hap) count (n) and their coverage across the genome assembly is shown as a percent. Haplotype lengths are described by Hap N_max (the maximum haplotype length found) and Hap N₅₀ (the shortest haplotype length that includes ≥ 50% of haplotype sequence.). Switch Errors (SE), Switch Error Rate (SER), Quality Adjusted N50 (QAN50) and Computational Time were calculated and compared as described in methods (code to calculate these values are part of HaplotypeTools)

ISSN: 1471-2105