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

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