The setQualityParam command allows you to adjust the parameters used for quality trimming. In order to be applied, the trimEnds parameter for the assemble command must be set to ‘true.’
| Parameter | Description | Allowed values |
|---|---|---|
| EndRegion | The number of bases at the end of a sequence considered to be the “end region” which is used by other quality parameters. | [number from 1-100] Default = 5 |
| MaxN | The maximum number of “N” bases permitted in the window used for N-based quality trimming. | [number from 1-100] Default = 2 |
| MaxNHiQual | The maximum number of “N” bases permitted in the window used for N-based quality trimming to meet the high-quality threshold. | [number from 0-100] Default = 1 |
| MinAveHiQual | The minimum averaged quality score of the evaluated window required to be considered high-quality. | [number from 10-40] Default = 22 |
| MinAveLowQual | The minimum averaged quality score of the evaluated window required to be considered low-quality. Wizard equivalent: Advanced Trim/Scan Options > Minimum quality. | [number from 5-40] Default = 20 |
| MinEndBaseQual | The minimum quality base score required in the specified end region. | [number from 5-40] Default = 15 |
| NTrimWinLength | The length of the window used for “N-based” quality trimming. N-based quality trimming trims bases that are called “N” and is used only when quality scores are not available. | [number from 5-100] Default = 7 |
| WinLength | The length of the window used for averaging quality scores. Wizard equivalent: Advanced Trim/Scan Options > Window. | [number from 2-100] Default = 5 |
Example:
setQualityParam winLength:30
setQualityParam minAveLowQaul:14
setQualityParam minAveHiQaul:18
setQualityParam minEndBaseQaul:15
setQualityParam endRegion:15
setQualityParam nTrimWinLength:50
setQualityParam maxN:2
setQualityParam maxNHiQual:1
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