Escherichia coli K12 MG1655. The E. coli MG1655 consists of a circular chromosome of 4,639,675 bp in length.
Read source
- The paired-end illuminia read data of E. coli were downloaded from Illumina (|Illumina) with a median insert size of 214 bp. More than 28.4 M reads
Sequence assembly
| Software |
Version |
Parameters |
Download |
| ABySS |
1.3.0 |
k=75 |
Abyss |
| Velvet |
1.1.04 |
VelvetOptimiser --s 59 --e 97 |
Velvet |
| Edena |
3 |
m=75 |
Edena |
| SOAPdenovo |
1.05 |
k=75 M=3 avg_ins=215 |
SOAPdenovo |
Merged File: E100_Contigs
Contig integrator
| Integrator |
Download |
| CISA |
CISA |
| minimus2 |
minimus2(AEVS),minimus2(ASEV), minimus2(ASVE),minimus2(ESAV),minimus2(ESVA),minimus2(SEAV),minimus2(SEVA),minimus2(SVAE),minimus2(VASE),minimus2(VEAS), |
Evaluation
- Eshcherichia coli K12 MG1655
- Evaluate by Mauve Assembly Metrics
- How to score genome assemblies using the Mauve system
- Score with Mauve metrics:
| Name |
NumContigs |
NumAssemblyBases |
DCJ_Distance |
NumMisCalled |
NumUnCalled |
NumGapsRef |
NumGapsAssembly |
TotalBasesMissed |
%Missed |
ExtraBases |
%Extra |
BrokenCDS |
IntactCDS |
ContigN50 |
ContigN90 |
MaxContigLength |
Blast_IntactCDS |
| Velvet |
1152 |
2775301 |
1124 |
49 |
0 |
1010 |
866 |
89319 |
3.1438 |
15087 |
0.5436 |
230 |
2421 |
5337 |
1329 |
22892 |
2265 |
| ABySS |
929 |
2769174 |
898 |
41 |
0 |
796 |
601 |
95493 |
3.3611 |
8641 |
0.312 |
171 |
2480 |
7793 |
1635 |
32717 |
2364 |
| Edena |
931 |
2757686 |
882 |
9 |
0 |
705 |
711 |
99275 |
3.4942 |
6966 |
0.2526 |
188 |
2463 |
6962 |
1672 |
37100 |
2331 |
| SOAPdenovo |
944 |
2781524 |
917 |
47 |
0 |
853 |
597 |
79607 |
2.802 |
11796 |
0.4241 |
166 |
2485 |
6386 |
1614 |
26967 |
2371 |
| CISA |
665 |
2776133 |
635 |
48 |
0 |
571 |
388 |
79805 |
2.8089 |
5675 |
0.2044 |
100 |
2551 |
10533 |
2460 |
42008 |
2463 |
| Minimus2(EVAS) |
569 |
2769617 |
559 |
71 |
0 |
531 |
402 |
85573 |
3.012 |
7624 |
0.2753 |
107 |
2544 |
10672 |
2578 |
42022 |
2468 |
