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.
|assembleBlocks||Specifies whether the assembly is a reference guided assembly.||[ true / ]|
|contamScan||If true, sequences will be scanned for the specified contaminant sequences before assembling. Also see loadContaminant||[ true / ]|
|doAssemble||If false, only the preprocessing will be done, and the sequences will not be assembled.||[ / false ]|
|repeatScan||If true, sequences will be scanned for the specified known repetitive sequences before assembling. Also see loadRepeat||[ true / ]|
|trimEnds||If true, the sequences will be trimmed based on quality scores before assembling. Wizard equivalent: Read options > Quality end trim.||[ true / ]|
|vectScan||If true, the sequences will be scanned and trimmed for vector before assembling. Also see loadVector.||[ true / ]|
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