Skip to main content

Table 2 Responses in the de-novo assembly case

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

Response Abbr. Criterion Low/high limita Target Defaultb Optimized
Total sequence in assembly (bp) tSeq Maximize 1,830,000 1,894,157 1,835,427 1,864,165
Number of contigs in assembly nSeq Minimize 95 85 91 89
N50 N50 Maximize 28,000 35,000 28,149 31,847
  1. The three responses that were measured in the de-novo assembly case are described above. a: Responses that have the criterion maximize have a low limit, and those with the criterion minimize have a high limit. b: Default values are based on using a k-mer size of 31 and leaving all other parameters unchanged