Ecoli
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)
| Abyss parameter | Download |
| k=29 | Abyss_k29 |
| k=31 | Abyss_k31 |
| k=33 | Abyss_k33 |
Merged File: Set2_Contig
- Set3 (Different parameters for SOAPdenovo - the assembler provides the largest number of contigs in Set1)
| SOAPdenovo parameter | Download |
| k=29 | SOAP_k29 |
| k=31 | SOAP_k31 |
| k=33 | SOAP_k33 |
Merged File: Set3_Contig
Contig integrator
- CISA
| Input | Download |
| Set1 | CISA_Set1 |
| Set2 | CISA_Set2 |
| Set3 | CISA_Set3 |
| Set2+Set3 | CISA_Set2&3 |
- minimus2
| Input | Download |
| Set1 | minimus2_Set1 |
Evaluation
- Benchmark genome
- Evaluate by Mauve Assembly Metrics
How to score genome assemblies using the Mauve system
Set1