The first two columns of the table below show the applicable SeqMan NGen wizard screen and setting name. The third column shows the equivalent scripting parameter. Each parameter is described in detail in SNG commands.

Wizard Screen Wizard Setting Equivalent SNG Scripting Parameter
Advanced Assembly Options (de novo) Default quality DefaultQuality
Default template quality TemplateDefaultQuality
Gap penalty GapPenalty
Match repeat percent MatchRepeatPercent
Match score MatchScore
Match spacing MatchSpacing
Match window MatchWindowLength
Max gap MaxGap
Max usable MaxUsableCount
Maximum coverage MaxAssemblyCoverage
Mismatch penalty MismatchPenalty
SNP low cover cutoff LowCoverageThreshold
SNP match percent SNPMatchPercentage
SNP passes SNPPasses
Advanced Trim/Scan Options 3’ trim end3
3’ value is measured from 5’end N/A
5’ trim end5
Flag length MinFlagLength
Mer length MerLength
Minimum matches MinMerMatch
Minimum quality MinAveLowQual
Trim length MinTrimLength
Trim to end EndCutOff
Window WinLength
Assembly Options (de novo, special reference-guided) Mer size MatchSize
Minimum length minLength
Minimum match percentage MinMatchPercent
Minimum sequences minSeqs
Realign reads after assembly SkipRealign
Remove small contigs after assembly N/A
Repeat handling UseRepeatHandling
Input Sequence Files (choose 454 and enter paired data) N/A
Read Options Contaminant scan N/A
Maximum total reads N/A
Quality end trim trimEnds
Repeat scan N/A
Vector/adaptor scan N/A
Assembly Output (de novo, special reference-guided) Save unassembled reads Assemble Boneyard
Your assembly is ready to begin N/A N/A

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