From: CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing
Tool | dataset (# reads) | # merges | # correct merges | time (sec) | accuracy | F 1 | dataset (# reads) | # merges | # correct merges | time (sec) | accuracy | F 1 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
CASPER | Â | 999,936 | 967,842 | 30 | 0.968 | 0.984 | Â | 713,782 | 667,421 | 23 | 0.932 | 0.965 |
COPE | A4 | 262,661 | 241,630 | 183 | 0.242 | 0.389 | C1 | 603,357 | 572,885 | 205 | 0.800 | 0.889 |
FLASH | (1,000,000) | 989,960 | 732,040 | 20 | 0.732 | 0.845 | (716,366) | 688,730 | 601,561 | 22 | 0.840 | 0.913 |
PANDAseq | Â | 991,698 | 807,691 | 6 | 0.808 | 0.894 | Â | 693,518 | 590,898 | 5 | 0.825 | 0.904 |
CASPER | Â | 999,973 | 997,201 | 30 | 0.997 | 0.999 | Â | 1,345,759 | 1,233,831 | 40 | 0.914 | 0.955 |
COPE | A5 | 924,634 | 915,981 | 205 | 0.916 | 0.956 | C2 | 1,105,743 | 1,046,420 | 319 | 0.775 | 0.873 |
FLASH | (1,000,000) | 999,578 | 977,355 | 19 | 0.977 | 0.989 | (1,350,602) | 1,282,916 | 1,101,436 | 35 | 0.816 | 0.898 |
PANDAseq | Â | 999,101 | 978,527 | 6 | 0.979 | 0.989 | Â | 1,298,903 | 1,080,593 | 9 | 0.800 | 0.889 |
CASPER | Â | 1,000,000 | 960,986 | 29 | 0.961 | 0.980 | Â | 671,877 | 658,631 | 19 | 0.977 | 0.989 |
COPE | S4 | 262,107 | 230,595 | 181 | 0.231 | 0.375 | PA | [COPE does not run on PA] | ||||
FLASH | (1,000,000) | 999,964 | 697,867 | 18 | 0.698 | 0.822 | (673,845) | 660,984 | 634,261 | 16 | 0.941 | 0.970 |
PANDAseq | Â | 999,976 | 785,919 | 5 | 0.786 | 0.880 | Â | 660,593 | 635,663 | 4 | 0.943 | 0.971 |
CASPER | Â | 1,000,000 | 997,303 | 28 | 0.997 | 0.999 | Â | Â | Â | Â | Â | Â |
COPE | S5 | 974,219 | 961,366 | 162 | 0.961 | 0.980 | Â | Â | Â | Â | Â | Â |
FLASH | (1,000,000) | 999,921 | 977,431 | 19 | 0.977 | 0.989 | Â | Â | Â | Â | Â | Â |
PANDAseq | Â | 999,947 | 976,701 | 6 | 0.977 | 0.988 | Â | Â | Â | Â | Â | Â |