Table 6 The efficiency of tandem repeats reconstruction from simulated data
From: De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
Sequence len. [bp] | Motif len. [bp] | Min. cov. (Eq. 5) | Unitigs | Scaffolds | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
ABySS | Velvet | SPAdes | dnaasm | ABySS | Velvet | SPAdes | dnaasm | |||
200 | 100 | 26 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 | 2/0/2 | 2/2/2 | 2/2/2 | 2/2/2 |
300 | 100 | 44 | 0/0/0 | 0/0/0 | 0/0/0 | 4/3/3 | 0/0/2 | 0/0/0 | 2/2/2 | 4/3/3 |
400 | 100 | 62 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 | 0/0/2 | 0/0/0 | 2/2/2 | 4/4/4 |
500 | 100 | 80 | 0/0/0 | 0/0/0 | 0/0/0 | 6/6/5 | 0/0/2 | 0/0/0 | 2/2/2 | 6/6/5 |
400 | 200 | 31 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 | 0/0/0 | 2/2/2 | 2/2/2 | 2/2/2 |
600 | 200 | 49 | 0/0/0 | 0/0/0 | 0/0/0 | 4/3/3 | 0/0/0 | 0/0/0 | 2/2/2 | 4/3/3 |
800 | 200 | 66 | 0/0/0 | 0/0/0 | 0/0/0 | 3/4/4 | 0/0/0 | 0/0/0 | 2/2/2 | 3/4/4 |
1000 | 200 | 84 | 0/0/0 | 0/0/0 | 0/0/0 | 6/6/5 | 0/0/0 | 0/0/0 | 2/2/2 | 6/6/5 |
600 | 300 | 32 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 |
900 | 300 | 50 | 0/0/0 | 0/0/0 | 0/0/0 | 3/3/3 | 0/0/0 | 0/0/0 | 2/2/2 | 3/3/3 |
1200 | 300 | 68 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 | 0/0/0 | 0/0/0 | 2/2/2 | 4/4/4 |
1500 | 300 | 86 | 0/0/0 | 0/0/0 | 0/0/0 | 5/5/5 | 0/0/0 | 0/0/0 | 2/2/2 | 5/5/5 |
800 | 400 | 33 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 |
1200 | 400 | 51 | 0/0/0 | 0/0/0 | 0/0/0 | 3/3/3 | 0/0/0 | 0/0/0 | 0/0/0 | 3/3/3 |
1600 | 400 | 69 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 |
2000 | 400 | 87 | 0/0/0 | 0/0/0 | 0/0/0 | 5/5/5 | 0/0/0 | 0/0/0 | 0/0/0 | 5/5/5 |
1000 | 500 | 33 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 | 0/0/0 | 0/0/0 | 2/2/2 | 2/2/2 |
1500 | 500 | 51 | 0/0/0 | 0/0/0 | 0/0/0 | 3/3/3 | 0/0/0 | 0/0/0 | 0/0/0 | 3/3/3 |
2000 | 500 | 69 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 | 0/0/0 | 0/0/0 | 0/0/0 | 4/4/4 |
2500 | 500 | 87 | 0/0/0 | 0/0/0 | 0/0/0 | 5/5/5 | 0/0/0 | 0/0/0 | 0/0/0 | 5/5/5 |