S. aureu 101 bp

Revision as of 25 February 2013 23:35 by admin (Comments | Contribs) | (→Evaluation)

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.

Read source

The paired-end illuminia read data of S. aureus were downloaded from Gage with a median insert size of 180 bp. More than 1.2 M reads

Sequence assembly

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

Contig integrator

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.

Evaluation

' Mauve assembly metrics ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' in this study GAGE ' ' ' '
Name NumContigs NumAssemblyBases DCJ_Distance NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed %Missed ExtraBases %Extra BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength Blast_IntactCDS Units(>200) N50 cor.Units cor.N50 Errors,(Indel>=5,Inv,Rel)
Abyss 133 4626205 107 334 69 123 119 57847 1.2468 29424 0.636 57 4263 96157 26096 222425 4249 108 96511 116 92933 8,(6,0,2)
CLC 379 4546926 304 100 0 288 287 130550 2.8138 3405 0.0749 62 4258 29767 8447 107342 4228 288 28450 290 28036 2,(0,1,1)
Edena 211 4569446 154 17 0 129 125 86780 1.8704 2078 0.0455 66 4254 54405 13642 186686 4191 182 54405 186 52796 4,(2,1,1)
SOAPdenovo 553 4547211 475 36 0 461 412 124407 2.6814 6972 0.1533 100 4220 17902 5384 103369 4131 450 17892 451 17892 1,(0,0,1)
Velvet 283 4550675 207 138 0 208 203 116542 2.5119 2783 0.0612 74 4246 52474 12537 166094 4194 217 52474 224 49022 8,(5,0,3)
CISA_Set1 72 4627549 70 241 50 91 92 49487 1.0666 32028 0.6921 44 4276 119107 32288 312018 4276 72 126254 83 113511 11,(8,0,3)
GAA# 314 4578451 245 148 7 240 227 97081 2.0924 10516 0.2284 72 4248 49430 13068 157184 4205 249 50305 251 48138 4,(2,0,2)
GAA* 311 4602917 224 156 3 225 216 93476 2.0147 11942 0.2591 76 4244 49990 12208 163308 4208 245 51075 238 47954 5,(3,0,2)
MAIA 110 4513348 96 82 54 100 95 129936 2.8005 1090 0.0242 48 4272 112717 30950 312145 4212 95 126075 97 107674 5,(2,0,3)
minimus2# 155 4598769 133 206 0 143 138 90163 1.9433 32604 0.7058 58 4262 82947 21666 202745 4243 137 85880 144 80493 8,(5,1,2)
minimus2* 73 4597392 67 323 0 96 80 155862 3.3593 102792 2.2503 52 4268 121942 35207 296685 4199 72 127420 83 113511 11,(7,1,3)
GAA (Abyss,Edena) 133 4637982 102 328 93 118 112 54835 1.1819 28888 0.6229 57 4263 96157 26096 222425 4258 108 96511 115 92933 8,(6,0,2)
GAA (A,C,E,S,V) 138 4639673 103 305 93 119 113 54254 1.1693 29292 0.6311 57 4263 96157 26096 222425 4258 108 96511 115 92933 8,(6,0,2)
MAIA (split3) 3 4915920 3 68 9573 89 90 213328 4.5979 464447 9.4478 55 4265 1422748 1422748 1927448 4217 - - - - -
MAIA (split3&n) 145 4800506 112 68 66 116 110 159557 3.439 124964 2.6031 50 4270 126075 30950 318482 4212 121 145106 103 107674 5,(3,0,2)
minimus2(A,C,E,S,V) 74 4608653 68 285 0 97 78 76881 1.657 35464 0.7695 50 4270 126075 34542 417704 4262 73 134584 83 113511 10,(7,1,2)
minimus2(S,C,V,E,A) 69 4215087 69 214 249 90 78 548181 11.8151 113137 2.6841 51 4269 119108 35441 312145 3855 69 115198 79 105796 10,(5,2,3)
  • Benchmark genome
S. aureus USA300_TCH1516
  • Evaluated by Mauve Assembly Metrics to calculate the values for the left columns of "Blast_IntactCDS"
How to score genome assemblies using the Mauve system
  • Evaluated by Blast with Features
  • Evaluated by GAGE to calculate the values for the right columns of "Blast_IntactCDS"
Gage
  • Score with Mauve metrics:
Name NumContigs NumAssemblyBases DCJ_Distance NumMisCalled NumUnCalled NumGapsRef NumGapsAssembly TotalBasesMissed %Missed ExtraBases %Extra BrokenCDS IntactCDS ContigN50 ContigN90 MaxContigLength 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 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 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 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 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 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 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 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 2390 - - - - -
MAIA (split4&n) 505 2859291 498 105 120 478 407 103565 3.5674 24695 0.8637 141 2552 12570 3840 52790 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 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 2468 299 16473 319 15528 22,(6,7,9)

[#] 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).