Staphylococcus aureus strain USA300_TCH1516. The S. aureu USA300_TCH1516 consists of a circular chromosome of 2,872,915 bp and two plasmid of 3,125 bp and 27,041 bp in length, respectively.
Software | Version | Parameters |
ABySS | 1.3.0 | k=41 |
Velvet | 1.1.04 | VelvetOptimiser --s 29 --e 97 |
Edena | 3 | m=41 |
SOAPdenovo | 1.05 | k=41 M=3 avg_ins=170 |
The name of merged file: Merged_ctg.fa
All Contigs
Beacuase minimus2 and GAA merge two assemblies at a time, we iteratively integrate the four assemblies in random order.
minimus2: A_E_V_S, E_V_S_A, E_S_V_A, E_V_A_S, S_V_E_A, S_A_V_E, S_E_A_V, V_A_S_E, V_E_A_S, V_S_E_A
GAA: A_S_E_V, A_V_E_S, A_E_V_S, E_A_V_S, E_V_S_A, S_E_A_V, S_V_A_E, V_S_A_E, V_A_E_S, V_A_S_E
The split references for MAIA and the integrated results can be downloaded maia_staphy_100.
Name | NumContigs | NumAssemblyBases | DCJ_Distance | NumMisCalled | NumUnCalled | NumGapsRef | NumGapsAssembly | TotalBasesMissed | %Missed | ExtraBases | %Extra | BrokenCDS | IntactCDS | ContigN50^ | ContigN90 | MaxContigLength | N50^ | Blast_IntactCDS | Units(>200) | N50^ | cor.Units | cor.N50^ | Errors,(Indel>=5,Inv,Rel) |
Abyss | 659 | 2854631 | 590 | 132 | 6 | 436 | 499 | 70014 | 2.4117 | 7077 | 0.2479 | 207 | 2486 | 9223 | 2512 | 35459 | 9229 | 2305 | 548 | 9154 | 554 | 9115 | 7,(2,0,5) |
Edena | 3287 | 2557545 | 3143 | 224 | 1 | 2957 | 3033 | 390614 | 13.4552 | 15975 | 0.6246 | 784 | 1909 | 1256 | 359 | 8680 | 1256 | 1053 | 2679 | 1073 | 2680 | 1072 | 4,(1,0,3) |
SOAPdenovo | 674 | 2872327 | 522 | 85 | 1 | 482 | 437 | 71040 | 2.4471 | 10463 | 0.3643 | 154 | 2539 | 9626 | 3069 | 47607 | 9762 | 2361 | 509 | 9626 | 511 | 9626 | 3,(2,0,1) |
Velvet | 502 | 2858949 | 432 | 153 | 12 | 377 | 386 | 69466 | 2.3928 | 7682 | 0.2687 | 137 | 2556 | 12962 | 3811 | 54726 | 13005 | 2421 | 405 | 12685 | 422 | 12217 | 19,(10,4,5) |
CISA | 347 | 2866024 | 330 | 266 | 15 | 316 | 278 | 60323 | 2.0779 | 11406 | 0.398 | 121 | 2572 | 14992 | 4664 | 54747 | 15327 | 2482 | 322 | 14916 | 343 | 14743 | 20,(6,5,9) |
GAA# | 1287 | 2798306 | 1166 | 191 | 6 | 1069 | 1084 | 144098 | 4.9636 | 12985 | 0.4691 | 322 | 2371 | 8319 | 2459 | 36637 | 8374 | 2045 | 1035 | 8209 | 1040 | 8095 | 9,(4,1,4) |
GAA* | 1150 | 2827068 | 1022 | 219 | 7 | 970 | 952 | 123336 | 4.24845 | 17517 | 0.6216 | 292 | 2401 | 8977 | 2614 | 38358 | 9026 | 2123 | 919 | 8943 | 925 | 8835 | 10,(4,2,4) |
MAIA (split4) | 4 | 2924771 | 6 | 127 | 6767 | 504 | 505 | 87938 | 3.0291 | 115881 | 3.9621 | 146 | 2547 | 1426408 | 5502 | 1464437 | 1464437 | 2390 | - | - | - | - | - |
MAIA (split4&n) | 505 | 2859291 | 498 | 105 | 120 | 478 | 407 | 103565 | 3.5674 | 24695 | 0.8637 | 141 | 2552 | 12570 | 3840 | 52790 | 12800 | 2376 | 404 | 12469 | 401 | 11838 | 2,(1,0,1) |
minimus2# | 421 | 2863142 | 399 | 206 | 1 | 359 | 343 | 70296 | 2.4214 | 15467 | 0.5400 | 142 | 2552 | 13049 | 3951 | 50951 | 13159 | 2425 | 396 | 13042 | 408 | 12725 | 13,(5,2,6) |
minimus2* | 302 | 2852733 | 302 | 276 | 1 | 308 | 272 | 90585 | 3.12 | 26239 | 0.92 | 114 | 2579 | 16577 | 5117 | 54766 | 16835 | 2468 | 299 | 16473 | 319 | 15528 | 22,(6,7,9) |
[^] Please note that the ContigN50 calculated by Mauve Assembly Metrics is incorrect (off-by-one error). We have followed the definition of N50 (A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. ref) to calculate N50s. As stated in GAGE, GAGE's N50 was calculated using the total reference genome length rather than the sum total of contig lengths. The GAGE's cor.N50 values were computed after correcting contigs by breaking them at each error.
[#] Please note that GAA and minimus2 were designed to merge two assemblies at a time, we thus performed all runs and took the average scores.
[*] Please note that the scores of minimus2 and GAA were taken from the average of ten random combinations (details).