The assemble command is required and reprocesses and assembles the sequences that have been loaded. Preprocessing may include quality trimming, and scanning for vector, repetitive, and contaminant sequences.
| Parameter | Description | Allowed values |
|---|---|---|
| assembleBlocks | Specifies whether the assembly is a reference guided assembly. | [ true / false ] |
| contamScan | If true, sequences will be scanned for the specified contaminant sequences before assembling. Also see loadContaminant | [ true / false ] |
| doAssemble | If false, only the preprocessing will be done, and the sequences will not be assembled. | [ true / false ] |
| repeatScan | If true, sequences will be scanned for the specified known repetitive sequences before assembling. Also see loadRepeat | [ true / false ] |
| trimEnds | If true, the sequences will be trimmed based on quality scores before assembling. Wizard equivalent: Read options > Quality end trim. | [ true / false ] |
| vectScan | If true, the sequences will be scanned and trimmed for vector before assembling. Also see loadVector. | [ true / false ] |
Example:
assemble
trimEnds:false
vectScan:false
repeatScan:false
contamScan:false
doAssemble:true
Need more help with this?
Contact DNASTAR