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Table 1 Factors in the de-novo assembly case

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

Parameter Abbr. Type Min Max Default Optimized
Size of k-mer (k) KMER Ordinal 20 90 31a 38
Minimum mean k-mer coverage of a unitig (c) MIKC Quantitative 2 15 sqrt (median)b 8.5
Minimum alignment length of a read (l) MIAL Ordinal 20 60 40 30
Minimum number of pairs required for building contigs (n) MIPA Ordinal 5 15 10 15
  1. The four factors investigated in the de-novo assembly case are described above. The letter in parenthesis following the parameter name is the parameter used in the abyss-pe command line interface. Min and max values define the design space. a: There is no default value explicitly specified by the ABySS documentation. However here we used a k-mer size of 31 for comparison purposes. b: This refers to the square root of the median k-mer coverage, which is affected by the sequencing depth and choice of k-mer size. The optimized values are the combination of factor values that produced the best outcome, as found by doepipeline