Table 3.
E. coli (SRR001665) 24-tile assembly results in terms of contiguity, accuracy, and statistics.
| Evaluations | Continuity | Accuracy | Statistics | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Contig # | NG50 (kbp) | NG50 corr. (kbp) | SNP | Indels | Misjoins | Asm. (%) | Unaligned ref. (%) | Duplicated ref. (%) | |
| Velvet 25k | 147 | 87.0 | 67.3 | 238 | 37 | 2 | 97.89 | 0.56 | 0.01 |
| Tiger-Velvet-R 51i | 281 | 95.6 | 87.2 | 190 | 35 | 3 | 100.92 | 0.14 | 2.30 |
| Tiger-Velvet-I 7i | 276 | 95.4 | 87.2 | 211 | 33 | 12 | 100.40 | 0.12 | 1.68 |
| SOAPdenovo 27k | 450 | 17.9 | 17.9 | 12 | 4 | 1 | 97.56 | 1.31 | 0.00 |
| Tiger-Soap-R 80i | 524 | 25.6 | 25.6 | 31 | 11 | 3 | 98.67 | 1.20 | 0.78 |
| Tiger-Soap-I 7i | 509 | 25.8 | 25.8 | 23 | 6 | 2 | 98.78 | 0.80 | 0.64 |
The columns include the number of contigs, NG50 size and its error-corrected size, the number of single nucleotide polymorphisms (SNPs), the number of indels and misjoins in contigs, total assembly length, genome coverage (100 - Unaligned ref.), and duplications. K-mer 25 and 27 are the best k-mer sizes for Velvet and SOAPdenovo, respectively. "#k" stands for the applied k-mer size. "#i" stands for the iteration number. Both Tiger-Velvet-I and Tiger-Soap-I evaluations use the best results from Velvet and SOAPdenovo as input, respectively.