The following commands can be used in the script for an SNG assembly. Click on the name of a command in the table below (shown in alphabetical order) to see a description and example, and to see the parameters associated with that command. All SNG commands and parameters are assumed to be optional unless the description states that it is required.

To see how SNG commands and parameters map to equivalent SeqMan NGen wizard settings, see Equivalence between wizard settings and SNG scripting commands.

Project management File loading Parameter settings Preprocessing and assembling
closeProject load454PairedEnd setContaminantParam appendToAssembly
runScript loadConstraint setContaminantParam assemble
saveProject loadContaminant setParam convertReads
saveReport loadLayout setQualityParam extendContigs
writeUnassembledSeqs loadRepeat setRepeatParam fixedTrim
loadSeq setVectorParam include
loadTemplate makeSeqNamesUnique
loadVector realignContigs
openProject removeSmallContigs
setDefaultDirectory set
setAssemblyReport
setPairSpecifier
splitLinkerReads
splitMIDSeqs
splitPairs
splitTemplates
trimVector

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