R. sphaeroides
Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosome of 3,188,609 bp and 943,016 bp, and five plasmids of 114,045 bp, 114,178 bp, 105,284 bp, 100,828 bp and 37,100 bp in length, respectively.
Read source
- The paired-end illuminia read data of R. sphaeroides were downloaded from Gage-B
Sequence assembly
There are eight assemblers, ABySS, CABOG, MaSuRCA, MIRA, SGA, SOAPdenovo, SPAdes 2.5 and Velvet, used in the data, and the scaffolding results were downloaded from SPAdes website
Contig integrator
Evaluation
- Benchmark genome
- Evaluated by QUAST
- Score with QUAST: more detail
| Basic statisitcs | ABySS | CABOD | MaSuRCA | SGA | SOAPdenovo | SPAdes 2.5 | Velvet | CISA |
| # contigs | 382 | 131 | 52 | 733 | 185 | 40 | 143 | 35 |
| Largest contig | 71578 | 177098 | 241348 | 44874 | 204500 | 739647 | 236829 | 740054 |
| Total length | 4503182 | 3953489 | 4247061 | 4091078 | 4549335 | 4781613 | 4526809 | 4950301 |
| NG50 | 21441 | 40287 | 144812 | 7971 | 45133 | 518052 | 85272 | 523557 |
| Misassemblies | ||||||||
| # misassemblies | 2 | 6 | 5 | 0 | 3 | 9 | 17 | 24 |
| Misassembled contigs length | 24651 | 135726 | 40523 | 0 | 24631 | 1180527 | 564277 | 1850338 |
| Genome statistics | ||||||||
| Genome fraction (%) | 97.529 | 85.608 | 91.915 | 87.77 | 98.068 | 99.37 | 97.437 | 99.474 |
| # genes | 4030 + 275 part | 3685 + 128 part | 4036 + 38 part | 3348 + 592 part | 4046 + 307 part | 4347 + 23 part | 4068 + 265 part | 4358 + 19 part |
| # mismatches per 100 kbp | 4.83 | 10.51 | 12.48 | 3.22 | 5.98 | 5.82 | 13.11 | 6.42 |
| # indels per 100 kbp | 3.43 | 7.97 | 5.84 | 3.34 | 3.9 | 3.63 | 8.34 | 3.69 |
| # N's per 100kbp | 0 | 20.77 | 4.83 | 0 | 139.23 | 0 | 739.09 | 3.68 |