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