SPAdes - D3
We used Dataset 3, Streptococcus pneumoniae TIGR4
Evaluation
- Benchmark genome
- Evaluated by QUAST
- QUAST (QUAST v2.3)
- Running QUAST needs gene list and NC_003028.fna information. There are 2301 genes in total.
- Score with QUAST: With PacBio Long Reads [more detail]
| Basic statistics | Website Data | Raw Data |
| # contigs | 20 | 90 |
| Largest contig | 433183 | 423414 |
| Total length | 2157030 | 2239813 |
| N50 | 210016 | 365564 |
| Misassemblies | ||
| # misassemblies | 13 | 8 |
| Misassembled contigs length | 1358992 | 815978 |
| Mismatches | ||
| # mismatches per 100kbp | 26.66 | 31.5 |
| # indels per 100kbp | 4.52 | 2.89 |
| # N's per 100kbp | 727.2 | 414.9 |
| Genome statistics | ||
| Genome fraction (%) | 98.267 | 99.177 |
| Duplication ratio | 1.017 | 1.018 |
| # genes | 2244 + 25 part | 2269 + 21 part |
| NGA50 | 1198037 | 1338442 |
| Running Time | 1hr16m | 6hr 05m |
Misassemblies for Adobe reader.
- Score with QUAST: Without PacBio Long Reads [more detail]
| Basic statistics | Website Data | Raw Data |
| # contigs | 65 | 142 |
| Largest contig | 247182 | 362472 |
| Total length | 2176172 | 2192447 |
| N50 | 84287 | 81903 |
| Misassemblies | ||
| # misassemblies | 19 | 3 |
| Misassembled contigs length | 1114155 | 85063 |
| Mismatches | ||
| # mismatches per 100kbp | 20.9|18.33 | |
| # indels per 100kbp | 2.14 | 2.1 |
| # N's per 100kbp | 1305| | |
| Genome statistics | ||
| Genome fraction (%) | 98.798 | 97.204 |
| Duplication ratio | 1.022 | 1.019 |
| # genes | 2271 + 15 part | 2239 + 33 part |
| NGA50 | 403409 | 224016 |
| Running Time | 19m | 53m |
Misassemblies for Adobe reader.