The following commands can be used in the script for an XNG 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 XNG commands and parameters are assumed to be optional unless the description states that it is required.

assembleTemplate exportVCF pause
computeSNP extractPairs quit
createGenomeTemplate include removeDuplicateSeqs
diskPath loadAssembly runScript
dumpConsensus loadBAM set
dumpSNP mergeIonTorrentShortReads setDefaultDirectory
execute message setMachineMemory
exportSplits pairFilePattern setParam

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