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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