Table 1. Results from individual runs of dDocent and Stacks.
dDocent runs varied in the level of similarity used to cluster reference sequences: A (90%), B (96%), and C (99%). For Stacks, forward reads and reverse reads were separately processed with denovo_map.pl (Stacks version 1.08), using three different sets of parameters: A, minimum depth of coverage of two to create a stack, a maximum distance of two between stacks, and a maximum distance of four between stacks from different individuals; B, minimum depth of coverage of three to create a stack, a maximum distance of four between stacks, and a maximum distance of eight between stacks from different individuals; and C, minimum depth of coverage of three to create a stack, a maximum distance of four between stacks, and a maximum distance of 10 between stacks from different individuals. For dDocent, complex variants were decomposed into canonical SNP and Indel calls and Indel calls were filtered out. SNP calls were evaluated at different individual coverage levels: (i) total number of SNPs; (ii) number of SNPS called in 75%, 90%, and 99% at 3X coverage; (iii) number of SNPS called in 75% and 90% of individuals at 5X coverage; (iv) number of SNPS called in 75% and 90% of individuals at 10X coverage; and, (v) number of SNPS called in 75% and 90% of individuals at 20X coverage. Run times are in minutes. Results from forward and reverse reads of Stacks were combined for comparison with dDocent, which inherently calls SNPs on both reads.
| dDocent A | dDocent B | dDocent C | Stacks A | Stacks B | Stacks C | |
|---|---|---|---|---|---|---|
| Red snapper | ||||||
| Total 3X SNPS | 53,298 | 53,316 | 53,361 | 28,817 | 33,479 | 34,459 |
| 75% 3X SNPs | 21,195 | 20,990 | 20,724 | 4,150 | 5,735 | 5,728 |
| 90% 3X SNPs | 9,102 | 8,850 | 8,639 | 675 | 987 | 983 |
| 99% 3X SNPs | 78 | 47 | 15 | – | – | – |
| 75% 5X SNPs | 14,881 | 14,594 | 14,339 | 2,632 | 4,351 | 4,324 |
| 90% 5X SNPs | 5,021 | 4,925 | 4,785 | 179 | 579 | 574 |
| 75% 10X SNPs | 7,556 | 7,318 | 7,154 | 783 | 1,618 | 1,579 |
| 90% 10X SNPS | 1,414 | 1,340 | 1,286 | 7 | 48 | 47 |
| 90% IND 90% 5X | 10,267 | 10,026 | 9,798 | 806 | 1,807 | 1,079 |
| 90% IND 90% 10x | 4,242 | 4,093 | 3,974 | 129 | 441 | 434 |
| Run time | 41 | 41 | 42 | 70 | 47 | 53 |
| Red drum | ||||||
| Total 3X SNPS | 46,378 | 46,688 | 46,832 | 45,792 | 50,821 | 52,366 |
| 75% 3X SNPs | 36,745 | 36,905 | 36,900 | 24,134 | 28,991 | 28,981 |
| 90% 3X SNPs | 32,356 | 32,424 | 32,330 | 13,439 | 17,946 | 17,874 |
| 99% 3X SNPs | 11,906 | 11,910 | 11,774 | 828 | 1,264 | 1,259 |
| 75% 5X SNPs | 34,279 | 34,393 | 34,336 | 21,021 | 26,526 | 26,464 |
| 90% 5X SNPs | 28,532 | 28,566 | 28,431 | 10,494 | 15,282 | 15,207 |
| 75% 10X SNPs | 27,523 | 27,605 | 27,488 | 12,928 | 17,018 | 16,983 |
| 90% 10X SNPS | 19,434 | 19,442 | 19,283 | 4,159 | 6,734 | 6,705 |
| 75% 20X SNPs | 15,080 | 15,111 | 14,981 | 2,276 | 3,538 | 3,516 |
| 90% 20X SNPs | 7,365 | 7,409 | 7,304 | 243 | 1,974 | 1,961 |
| Run time | 43 | 45 | 45 | 58 | 55 | 65 |
| Silk snapper | ||||||
| Total 3X SNPS | 68,668 | 68,825 | 68,861 | 48,742 | 55,505 | 58,352 |
| 75% 3X SNPs | 30,771 | 30,391 | 30,051 | 7,596 | 9,705 | 9,696 |
| 90% 3X SNPs | 14,952 | 14,673 | 14,415 | 2,007 | 3,439 | 3,433 |
| 99% 3X SNPs | 4,294 | 4,060 | 3,952 | 132 | 527 | 523 |
| 75% 5X SNPs | 20,534 | 20,188 | 19,968 | 4,789 | 7,290 | 7,274 |
| 90% 5X SNPs | 9,103 | 8,750 | 8,533 | 1,225 | 2,573 | 2,570 |
| 75% 10X SNPs | 9,765 | 9,400 | 9,159 | 2,094 | 3,547 | 3,546 |
| 90% 10X SNPS | 3,923 | 3,691 | 3,490 | 489 | 1,224 | 1,223 |
| 75% 20X SNPs | 4,069 | 3,832 | 3,624 | 703 | 1,415 | 1,411 |
| 90% 20X SNPs | 1,431 | 1,313 | 1,228 | 136 | 417 | 418 |
| Run time | 88 | 95 | 59 | 93 | 89 | 204 |