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

BMC Bioinformatics

Table 4 Factors in the k-mer classification case

Parameter	Abbr.	Type	Min	Max	Default	Optimized
Minimum k-mer hits	MH	Ordinal	1	200	^a	14
Standard deviation of the relative errors of the estimate	PRES	Ordinal	10	18	12	17
Minimum tax-ID score threshold	FILT	Quantitative	0	0.05	0	0

The three factors investigated in the k-mer case are described above. Min and max values define the design space. The optimized values are those that in combination produced the best outcome, as found by doepipeline. ^a: The KrakenUniq documentation to our knowledge does not state what the default value is

ISSN: 1471-2105