R. sphaeroides
Rhodobacter sphaeroides strain 2.4.1. The R. sphaeroides 2.4.1 consists of two circular chromosomes 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 illumina read data of R. sphaeroides were available at Gage-B.
Sequence assembly
We have downloaded scaffolding assemblies from SPAdes website.
Contig integrator
We have used CISA to integrate the assemblies and generated CISA's contigs.
Evaluation
- Benchmark genome
- Evaluated by QUAST
- QUAST (QUAST v2.1)
- Running QUAST needs gene and sequence information. There are 4388 genes in total.
- Score with QUAST: more detail.
| Basic statistics | 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 |
A dot plot (pdf) of CISA assembly against reference genome.