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 |
NumRefReplicons |
NumAssemblyBases |
NumReferenceBases |
NumLCBs |
DCJ_Distance |
NumDCJBlocks |
NumSNPs |
NumMisCalled |
NumUnCalled |
NumGapsRef |
NumGapsAssembly |
TotalBasesMissed |
PercBasesMissed |
ExtraBases |
PercExtraBases |
MissingChromosomes |
ExtraContigs |
NumSharedBoundaries |
NumInterLcbBoundaries |
BrokenCDS |
IntactCDS |
ContigN50 |
ContigN90 |
MinContigLength |
MaxContigLength |
| assembly1.fasta |
157 |
5 |
3920004 |
4012900 |
13 |
121 |
121 |
90 |
90 |
0 |
141 |
128 |
119928 |
2.9886 |
1818 |
0.0464 |
0 |
44 |
1 |
8 |
30 |
3908 |
123582 |
11735 |
100 |
217295 |
| assembly2.fasta |
1394 |
5 |
4394403 |
4012900 |
851 |
1652 |
1666 |
31356 |
925 |
30431 |
1848 |
1739 |
161388 |
4.0217 |
503214 |
11.4512 |
0 |
301 |
2 |
281 |
505 |
3433 |
843300 |
57 |
57 |
1354539 |
| assembly3.fasta |
367 |
5 |
3880100 |
4012900 |
68 |
400 |
400 |
7093 |
1209 |
5884 |
999 |
991 |
155857 |
3.8839 |
22465 |
0.579 |
0 |
1 |
1 |
37 |
442 |
3496 |
19349 |
5537 |
234 |
99636 |
|
