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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

From: HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

Tool Param Het. (/Kb) Read Length (nt, paired) Hap n Genome coverage (%) Hap Nmax 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
  1. Haplotype (Hap) count (n) and their coverage across the genome assembly is shown as a percent. Haplotype lengths are described by Hap Nmax (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)