Eshcherichia coli K12 MG1655
Read source
- The illuminia read data of E. coli (Paired-end sequencing library with 200 bp inserts) downloaded from Sequence Read Archive (SRA).
Sequence assembly
- Set1 (Different Assemblers)
| 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
- Set2 (Different parameters for Abyss - the assembler provides the lowest number of contigs in Set1)
Merged File: Set2_Contig
- Set3 (Different parameters for SOAPdenovo - the assembler provides the largest number of contigs in Set1)
Merged File: Set3_Contig
Contig integrator
Evaluation
- Eshcherichia coli K12 MG1655
- Evaluate by Mauve Assembly Metrics
- How to score genome assemblies using the Mauve system
| Name |
NumContigs |
NumAssemblyBases |
NumMisCalled |
NumUnCalled |
NumGapsRef |
NumGapsAssembly |
TotalBasesMissed |
PercBasesMissed |
ExtraBases |
PercExtraBases |
BrokenCDS |
IntactCDS |
ContigN50 |
ContigN90 |
MaxContigLength |
| Abyss |
133 |
4626205 |
334 |
69 |
123 |
119 |
57847 |
1.2468 |
29424 |
0.636 |
57 |
4263 |
96157 |
26096 |
222425 |
| CLC |
379 |
4546926 |
100 |
0 |
288 |
287 |
130550 |
2.8138 |
3405 |
0.0749 |
62 |
4258 |
29767 |
8447 |
107342 |
| Edena |
211 |
4569446 |
17 |
0 |
129 |
125 |
86780 |
1.8704 |
2078 |
0.0455 |
66 |
4254 |
54405 |
13642 |
186686 |
| SOAPdenovo |
553 |
4547211 |
36 |
0 |
461 |
412 |
124407 |
2.6814 |
6972 |
0.1533 |
100 |
4220 |
17902 |
5384 |
103369 |
| Velvet |
283 |
4550675 |
138 |
0 |
208 |
203 |
116542 |
2.5119 |
2783 |
0.0612 |
74 |
4246 |
52474 |
12537 |
166094 |
| CISA_Set1 |
81 |
4625471 |
229 |
73 |
92 |
93 |
54849 |
1.1822 |
32166 |
0.6954 |
46 |
4274 |
113510 |
29195 |
268608 |
| minimus2 |
74 |
4608653 |
285 |
0 |
97 |
78 |
76881 |
1.657 |
35464 |
0.7695 |
50 |
4270 |
126075 |
34542 |
417704 |
| Name |
NumContigs |
NumAssemblyBases |
NumMisCalled |
NumUnCalled |
NumGapsRef |
NumGapsAssembly |
TotalBasesMissed |
PercBasesMissed |
ExtraBases |
PercExtraBases |
BrokenCDS |
IntactCDS |
ContigN50 |
ContigN90 |
MaxContigLength |
| Abyss_k29 |
130 |
4634010 |
322 |
30 |
118 |
115 |
61835 |
1.3327 |
40405 |
0.8719 |
54 |
4266 |
95691 |
26567 |
268182 |
| Abyss_k31 |
133 |
4626205 |
334 |
69 |
123 |
119 |
57847 |
1.2468 |
29424 |
0.636 |
57 |
4263 |
96157 |
26096 |
222425 |
| Abyss_k33 |
135 |
4644184 |
354 |
338 |
139 |
119 |
66355 |
1.4302 |
44937 |
0.9676 |
78 |
4242 |
89001 |
24907 |
268398 |
| CISA_Set2 |
105 |
4635199 |
332 |
130 |
117 |
103 |
55567 |
1.1976 |
39517 |
0.8525 |
63 |
4257 |
113377 |
27272 |
222663 |
| SOAP_k29 |
1373 |
4582756 |
48 |
0 |
466 |
415 |
124372 |
2.6806 |
7247 |
0.1581 |
100 |
4220 |
17892 |
5276 |
103369 |
| SOAP_k31 |
1295 |
4583165 |
56 |
0 |
510 |
466 |
121606 |
2.621 |
9201 |
0.2008 |
121 |
4199 |
17003 |
4286 |
77302 |
| SOAP_k33 |
2170 |
4608265 |
105 |
0 |
1470 |
1380 |
126273 |
2.7216 |
41165 |
0.8933 |
507 |
3813 |
5391 |
1449 |
22953 |
| CISA_Set3 |
465 |
4546819 |
117 |
0 |
402 |
366 |
133247 |
2.8719 |
19266 |
0.4237 |
95 |
4225 |
21543 |
6065 |
103369 |
| CISA_Set2&3 |
105 |
4636783 |
351 |
160 |
118 |
104 |
54999 |
1.1854 |
39905 |
0.8606 |
60 |
4260 |
113377 |
27272 |
222663 |