Table 5 Comparative study of running time, percentage of reads aligned by different aligners for four datasets of E. coli-real, A. thaliana-real, O. sativa-real and S. cerevisiae-real
From: S-conLSH: alignment-free gapped mapping of noisy long reads
Dataset | #Reads | Mapper | Index time (s) | Mapping time (s) | % of reads aligned |
|---|---|---|---|---|---|
E. coli-real | 300 | Minimap | 1 | 1 | 91.6 |
Minimap2 | 2 | 2 | 100 | ||
lordFAST | 3 | 10 | 100 | ||
conLSH | 1 | 2 | 100 | ||
S-conLSH | 2 | 1 | 98.3 | ||
A. thaliana-real | 3,448,228 | Minimap | 7 | 798 | 88 |
Minimap2 | 6 | 10,562 | 100 | ||
lordFAST | 78 | 24,277 | 100 | ||
conLSH | 1 | 40,028 | 99.4 | ||
S-conLSH | 27 | 2073 | 93.7 | ||
O. sativa-real | 590,268 | Minimap | 20 | 487 | 94.3 |
Minimap2 | 20 | 6898 | 100 | ||
lordFAST | 287 | 10,462 | 100 | ||
conLSH | 6 | 18,024 | 97 | ||
S-conLSH | 88 | 962 | 98.2 | ||
S. cerevisiae-real | 594,243 | Minimap | 1 | 104 | 41.8 |
Minimap2 | 1 | 881 | 100 | ||
lordFAST | 7 | 2130 | 100 | ||
conLSH | 1 | 7890 | 99.8 | ||
S-conLSH | 3 | 299 | 90.3 |