Table 2.
N50 values and number of contigs (in parentheses) of 10 oral streptococcal genomes from various de novo assemblers and MyPro with CISA.
|
S. salivarius
|
S. sanguinis
|
S. mitis
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| UC3162 | I141 | VT517 | COL85/1862 | NCTC10712 | OP51 | SK141 | UC921A | UC5873 | UC6950A | |
| Abyss | 102,123 (44) | 205,597 (27) | 201,754 (34) | 258,394 (23) | 294,670 (13) | 325,986 (10) | 325,653 (11) | 224,590 (25) | 1,371,488 (26) | 140,468 (66) |
| Edena | 112,782 (36) | 79,082 (48) | 169,164 (47) | 190,728 (39) | 293,981 (16) | 321,991 (9) | 244,280 (13) | 224,608 (26) | 202,683 (43) | 137,264 (69) |
| Velvet | 93,598 (72) | 282,985 (23) | 202,625 (80) | 398,214 (33) | 293,951 (16) | 1,177,164 (15) | 1,229,524 (12) | 226,431 (22) | 1,380,504 (34) | 141,356 (88) |
| SOAPdenovo | 31,809 (166) | 79,987 (66) | 21,141 (307) | 36,934 (137) | 28,642 (143) | 84,194 (58) | 94,143 (54) | 41,314 (126) | 11,579 (376) | 28,278 (224) |
| SPAdes | 88,327 (69) | 292,810 (17) | 96,152 (91) | 335,392 (42) | 257,414 (20) | 79,761 (227) | 315,886 (13) | 223,855 (28) | 1,374,450 (27) | 95,372 (75) |
| MyPro (CISA) | 116,758 (25) | 331,769 (11) | 290,644 (25) | 722,753 (14) | 572,071 (10) | 1,183,284 (11) | 1,236,221 (6) | 226,881 (14) | 1,375,455 (12) | 142,219 (35) |
Higher N50 value and lower number of contigs are indicative of superior genome assembly. Note that in comparison with other genome assembly software, MyPro consistently demonstrates values indicative of superior genome assembly (highlighted in bold).