Table 3 Factors in the scaffolding case
Parameter | Abbr. | Type | Min | Max | Default | Optimized |
|---|---|---|---|---|---|---|
Minimum alignment length to allow a contig to be included for scaffolding (a) | ALEN | Ordinal | 0 | 5000 | 0 | 0 |
Minimum gap between two contigs (g) | GLEN | Ordinal | −3000 | 3000 | −200 | − 750 |
Maximum link ratio between two best contig pairs (r) | RRAT | Quantitative | 0.1 | 0.7 | 0.3 | 0.325 |
Minimum identity of the alignment of the long reads to the contig sequences (i) | IDEN | Ordinal | 30 | 90 | 70 | 82 |