Escherichia coli K12 MG1655. The E. coli MG1655 consists of a circular chromosome of 4,639,675 bp in length.
Software | Version | Parameters | Download |
ABySS | 1.3.0 | k=31 | Abyss |
Velvet | 1.1.04 | k=29 ins_length=215 cov_cutoff=12 exp_cov=24 min_contig_lgth=100 scaffolding=no | Velvet |
Edena | 3 | m=30 | Edena |
SOAPdenovo | 1.05 | K=29 M=3 | SOAPdenovo |
CLC | 4.7.2 | insert_size_range=194,236 minimum_contig_length=100 | CLC |
Merged File: Set1_Contig
Abyss parameter | Download |
k=29 | Abyss_k29 |
k=31 | Abyss_k31 |
k=33 | Abyss_k33 |
Merged File: Set2_Contig
SOAPdenovo parameter | Download |
k=29 | SOAP_k29 |
k=31 | SOAP_k31 |
k=33 | SOAP_k33 |
Merged File: Set3_Contig
Download |
CISA+SSPACE |
ABySS+SSPACE |
Minimus2+SSPACE |
Input | Download |
Set1 | CISA_Set1 |
Set2 | CISA_Set2 |
Set3 | CISA_Set3 |
Set2+Set3 | CISA_Set2_3 |
Set1+2+3+2_3 | CISA_Set1+2+3+2_3 |
The input file for CISA is an assembled set of contigs, e.g., the set1 contains the contigs obtained from Abyss, CLC, Edena, SOAPdenovo, and Velvet.
The integrated contigs generated by CISA can be directly downloaded via the Download link.
maia('./assembly_list.txt','./NC_000913.fna')
assembly_list.txt:
Edena ./Edena_contigs.fa 2 SOAP ./SOAP_contigs.fa 2 Velvet ./Velvet.fa 2 CLC ./CLC.fa 2 Abyss ./Abyss_contigs.fa 3
A file named maia_assembly.fa is generated, containing a draft genome of 4640055 bp with 126761 uncalled bases (Ns). We split the genome into contigs (at >10Ns) and got the set of contigs maia.fa.
Input | Download |
Set1 | minimus2_Set1(A,C,E,S,V) |
Set1 | minimus2_Set1(S,C,V,E,A) |
Since minimus2 can only merge two sequence sets at a time, we used minimus2 to integrate the set1 in alphabetical order (i.e., ACESV) and in descending order of contig number (i.e., SCEVA).
After formatting the contig names in the format of >Contig1.1, we conducting GAA by using
perl gaa.pl -t ../Abyss_contigs_1.fa -q ../CLC_1.fa -o AC
Set1
Name | NumContigs | NumAssemblyBases | DCJ_Distance | NumMisCalled | NumUnCalled | NumGapsRef | NumGapsAssembly | TotalBasesMissed | %Missed | ExtraBases | %Extra | BrokenCDS | IntactCDS | ContigN50 | ContigN90 | MaxContigLength | Blast_IntactCDS |
Abyss | 133 | 4626205 | 108 | 334 | 69 | 123 | 119 | 57847 | 1.2468 | 29424 | 0.636 | 57 | 4263 | 96157 | 26096 | 222425 | 4257 |
CLC | 379 | 4546926 | 304 | 100 | 0 | 288 | 287 | 130550 | 2.8138 | 3405 | 0.0749 | 62 | 4258 | 29767 | 8447 | 107342 | 4233 |
Edena | 211 | 4569446 | 154 | 17 | 0 | 129 | 125 | 86780 | 1.8704 | 2078 | 0.0455 | 66 | 4254 | 54405 | 13642 | 186686 | 4204 |
SOAPdenovo | 553 | 4547211 | 475 | 36 | 0 | 461 | 412 | 124407 | 2.6814 | 6972 | 0.1533 | 100 | 4220 | 17902 | 5384 | 103369 | 4146 |
Velvet | 283 | 4550675 | 207 | 138 | 0 | 208 | 203 | 116542 | 2.5119 | 2783 | 0.0612 | 74 | 4246 | 52474 | 12537 | 166094 | 4204 |
CISA_Set1 | 72 | 4627549 | 70 | 241 | 50 | 91 | 92 | 49487 | 1.0666 | 332028 | 0.6921 | 44 | 4276 | 119107 | 32288 | 312018 | 4290 |
MAIA | 110 | 4513348 | 96 | 82 | 54 | 100 | 95 | 129936 | 2.8005 | 1090 | 0.0242 | 48 | 4272 | 112717 | 30950 | 312145 | 4222 |
minimus2(A,C,E,S,V) | 74 | 4608653 | 68 | 285 | 0 | 97 | 78 | 76881 | 1.657 | 35464 | 0.7695 | 50 | 4270 | 126075 | 34542 | 417704 | 4268 |
minimus2(S,C,V,E,A) | 69 | 4215087 | 69 | 214 | 249 | 90 | 78 | 548181 | 11.8151 | 113137 | 2.6841 | 51 | 4269 | 119108 | 35441 | 312145 | 3869 |
GAA (Abyss,Edena) | 133 | 4637982 | 102 | 328 | 93 | 118 | 112 | 54835 | 1.1819 | 28888 | 0.6229 | 57 | 4263 | 96157 | 26096 | 222425 | 4267 |
GAA (A,C,E,S,V) | 138 | 4639673 | 103 | 305 | 93 | 119 | 113 | 54254 | 1.1693 | 29292 | 0.6311 | 57 | 4263 | 96157 | 26096 | 222425 | 4267 |
Set2-Set3
Name | NumContigs | NumAssemblyBases | DCJ_Distance | NumMisCalled | NumUnCalled | NumGapsRef | NumGapsAssembly | TotalBasesMissed | %Missed | ExtraBases | %Extra | BrokenCDS | IntactCDS | ContigN50 | ContigN90 | MaxContigLength | Blast_IntactCDS |
Abyss_k29 | 130 | 4634010 | 108 | 322 | 30 | 118 | 115 | 61835 | 1.3327 | 40405 | 0.8719 | 54 | 4266 | 95691 | 26567 | 268182 | 4267 |
Abyss_k31 | 133 | 4626205 | 107 | 334 | 69 | 123 | 119 | 57847 | 1.2468 | 29424 | 0.636 | 57 | 4263 | 96157 | 26096 | 222425 | 4257 |
Abyss_k33 | 135 | 4644184 | 106 | 354 | 338 | 139 | 119 | 66355 | 1.4302 | 44937 | 0.9676 | 78 | 4242 | 89001 | 24907 | 268398 | 4263 |
CISA_Set2 | 106 | 4635648 | 93 | 321 | 131 | 117 | 104 | 55343 | 1.1928 | 39776 | 0.858 | 64 | 4256 | 113377 | 27272 | 222663 | 4268 |
SOAP_k29 | 1373 | 4582756 | 479 | 48 | 0 | 466 | 415 | 124372 | 2.6806 | 7247 | 0.1581 | 100 | 4220 | 17892 | 5276 | 103369 | 4146 |
SOAP_k31 | 1295 | 4583165 | 519 | 56 | 0 | 510 | 466 | 121606 | 2.621 | 9201 | 0.2008 | 121 | 4199 | 17003 | 4286 | 77302 | 4094 |
SOAP_k33 | 2170 | 4608265 | 1519 | 105 | 0 | 1470 | 1380 | 126273 | 2.7216 | 41165 | 0.8933 | 507 | 3813 | 5391 | 1449 | 22953 | 3379 |
CISA_Set3 | 440 | 4532470 | 383 | 35 | 0 | 379 | 338 | 133920 | 2.8864 | 5809 | 0.1282 | 88 | 4232 | 23332 | 6264 | 103369 | 4165 |
CISA_Set2&3 | 105 | 4636952 | 91 | 344 | 159 | 117 | 103 | 57192 | 1.2327 | 40304 | 0.8692 | 60 | 4260 | 113377 | 27272 | 222663 | 4269 |
CISA_Set_1_2_3_2&3 | 72 | 4637760 | 72 | 554 | 53 | 112 | 100 | 43060 | 0.9281 | 37481 | 0.8082 | 44 | 4276 | 115185 | 35678 | 310691 | 4291 |
Name | NumContigs | NumAssemblyBases | DCJ_Distance | NumMisCalled | NumUnCalled | NumGapsRef | NumGapsAssembly | TotalBasesMissed | %Missed | ExtraBases | %Extra | BrokenCDS | IntactCDS | ContigN50 | MaxContigLength | Blast_IntactCDS |
CISA+SSPACE | 69 | 4627867 | 70 | 237 | 50 | 90 | 91 | 52150 | 1.124 | 37320 | 0.8064 | 44 | 4276 | 134584 | 418148 | 4290 |
Abyss+SSPACE | 101 | 4627104 | 89 | 393 | 735 | 114 | 119 | 54956 | 1.1845 | 33747 | 0.7293 | 57 | 4263 | 107040 | 268750 | 4272 |
minimus2+SSPACE | 64 | 4608774 | 64 | 337 | 54 | 93 | 76 | 75502 | 1.6273 | 36021 | 0.7816 | 49 | 4271 | 150458 | 420117 | 4268 |