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Table 3 Factors in the scaffolding case

From: doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows

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
  1. The four factors investigated in the scaffolding case are described above. The letter in parenthesis following the parameter name is the parameter used in the SSPACE command line interface. Min and max values define the design space. The optimized values are those that in combination produced the best outcome, as found by doepipeline