SPAdes - D1 and D5
We used Dataset 1, Escherichia coli K-12 MG1655 and with single SMRT cell long reads of Dataset 5 (m120208_071634)
spades.py --pe1-1 frq_1.fastq --pe1-2 frag_2.fastq --mp1-1 jump1_1.fastq --mp1-2 jump1_2.fastq --mp2-1 jump2_1.fastq --mp2-2 jump2_2.fastq
Evaluation
- Benchmark genome
- Evaluated by QUAST
- QUAST (QUAST v2.3)
- Running QUAST requires Ec_gene_list and NC_000913.fna. There are 4497 genes in total.
- Score with QUAST: With PacBio Long Reads [ more detail]
| Basic statistics | Website data | Raw Data | Raw Data with D5 single SMRT cell |
| # contigs | 16 | 28 | 23 |
| 1090659 | 1749262 | 3014973 | |
| Total length | 4611695 | 4630525 | 4634373 |
| N50 | 692096 | 1092719 | 3014973 |
| Misassemblies | |||
| # misassemblies | 5 | 3 | 1 |
| Misassembled contigs length | 1844546 | 2841981 | 3014973 |
| Mismatches | |||
| # mismatches per 100kbp | 9.36 | 8.62 | 8.7 |
| # indels per 100kbp |0.76 | 0.85 | 0.63 | |
| # N's per 100kbp | 92.46 | 31.31 | 7.94 |
| Genome statistics | |||
| Genome fraction (%) | 98.951 | 99.459 | 99.605 |
| Duplication ratio | 1.004 | 1.001 | 1.001 |
| # genes | 4459 + 13 part | 4470 + 13 part | 4479 + 3 part |
| NGA50 | 657193 | 694449 | 2497974 |
| Running Time | 27m | 1 hr 39m | 1hr 20m |
Misassemblies for Adobe reader.
- Score with QUAST: Without PacBio Long Reads [ more detail]
| Basic statistics | Website data | Raw Data |
| # contigs | 2 | 1 |
| Largest contig | 1087924 | 1190496 |
| Total length | 4604959 | 4612084 |
| N50 | 555967 | 693826 |
| Misassemblies | ||
| # misassemblies | 5 | 3 |
| Misassembled contigs length | 1294499 | 1190496 |
| Mismatches | ||
| # mismatches per 100kbp | 8.26 | 5.27 |
| # indels per 100kbp | 0.74 | 0.5 |
| # N's per 100kbp | 161.91 | 136.01 |
| Genome statistics | ||
| Genome fraction (%) | 98.951 | 98.939 |
| Duplication ratio | 1.004 | 1.002 |
| # genes | 4427 + 25 part | 4430 + 21 part |
| NGA50 | 368287 | 651327 |
| Running Time | 27m | 1hr 33m |
Misassemblies for Adobe reader.