SPAdes - D2
We used Dataset 2, Rhodobacter sphaeroides strain 2.4.1.
Evaluation
- Benchmark genome
- Evaluated by QUAST
- QUAST (QUAST v2.3)
- Running QUAST requires gene list and reference genome. There are 4388 genes in total.
- Score with QUAST: With PacBio Long Reads [more detail]
| Basic statistics | Website Data | Raw Data |
| # contigs | 57 | 44 |
| Largest contig | 1209840 | 1895290 |
| Total length | 4566203 | 4584163 |
| N50 | 318530 | 422736 |
| Misassemblies | ||
| # misassemblies | 33 | 10 |
| Misassembled contigs length | 3312932 | 1235058 |
| Mismatches | ||
| # mismatches per 100kbp | 53.46 | 37.73 |
| # indels per 100kbp | 23.18 | 8.02 |
| # N's per 100kbp | 203.41 | 79.88 |
| Genome statistics | ||
| Genome fraction (%) | 98.589 | 99.157 |
| Duplication ratio | 1.006 | 1.005 |
| # genes | 4170 + 166 part | 4287 + 68 part |
| NGA50 | 164917 | 331154 |
| Running Time | 27m | 1hr 39m |
Misassemblies for Adobe reader.
- Score with QUAST: Without PacBio Long Reads [more detail]
| Basic statistics | Website Data | Raw Data |
| # contigs | 31 | 57 |
| Largest contig | 3188995 | 3186675 |
| Total length | 4592561 | 4583750 |
| N50 | 3188995 | 3186675 |
| Misassemblies | ||
| # misassemblies | 9 | 6 |
| Misassembled contigs length | 4205887 | 4147900 |
| Mismatches | ||
| # mismatches per 100kbp | 5.81 | 4.233 |
| # indels per 100kbp | 5.64 | 3.57 |
| # N's per 100kbp | 120.74 | 149.31 |
| Genome statistics | ||
| Genome fraction (%) | 99.45 | 98.789 |
| Duplication ratio | 1.018 | 1.022 |
| # genes | 4348 + 27 part | 4313 + 47 part |
| NGA50 | 3182258 | 3180491 |
| Running Time | 1hr 19m | 1d 15hr 44m |
Misassemblies for Adobe reader.