The following table shows the parameters shown in the Phrap dialog along with the minimum, maximum, default values and the command line option it refers to.
|
Assembler Name |
Min |
Max |
Command line parameter |
default |
|
Pairwise alignments |
||||
|
"Mismatch penalty" |
-100L |
0L |
Penalty |
-2; |
|
"Gap initiation penalty" |
-100L |
0L |
GapInit |
Penalty-2; |
|
"Gap extension penalty" |
-100L |
0L |
GapExt |
Penalty-1; |
|
"Insertion gap penalty" |
-100L |
0L |
InsGapExt |
-3; |
|
"Deletion gap penalty" |
-100L |
0L |
DelGapExt |
-3; |
|
Banded Search |
||||
|
"Minimum match length" |
0L |
1000L |
MinMatch |
14; |
|
"Maximum match length" |
0L |
1000L |
MaxMatch |
30; |
|
"Minimum alignment score" |
0L |
1000L |
Raw |
false; |
|
"Maximum group size" |
0L |
1000L |
MaxGroupSize |
20; |
|
"Half bandwidth" |
-0L |
1000L |
Bandwidth |
14; |
|
Use Raw Word Lengths |
WordRaw |
false; |
||
|
Globality |
||||
|
Filtering |
||||
|
"Mask Level (%)" |
0L |
101L |
MaskLevel |
80; |
|
Min. Alignment score |
MinScore |
30; |
||
|
Phrap Basic Parameters |
Phrap Basic Defaults |
|||
|
Pairwise Alignments |
||||
|
"Mismatch penalty" |
-100L |
0L |
Penalty |
-2; |
|
"Gap initiation penalty" |
-100L |
0L |
GapInit |
Penalty-2; |
|
"Gap extension penalty" |
-100L |
0L |
GapExt |
Penalty-1; |
|
Banded Search |
||||
|
"Minimum match length" |
0L |
1000L |
MinMatch |
14; |
|
"Maximum match length" |
0L |
1000L |
MaxMatch |
30; |
|
Filtering |
||||
|
"Minimum alignment score" |
0L |
1000L |
MinScore |
30; |
|
"Potential vector bases" |
0L |
1000L |
VectorBound |
80; |
|
Assembly |
||||
|
"Stringency" |
0L |
10L |
Forcelevel |
0; |
|
"Maximum gap" |
0L |
1000L |
Maxgap |
30; |
|
"Repeat stringency" |
0.01f |
0.99f |
RepeatStringency |
0.95; |
|
Consensus |
||||
|
"Minimum segment size" |
0L |
1000L |
Node_Seg |
8; |
|
"Node spacing" |
0L |
1000L |
Node_Space |
4; |
|
Phrap Advanced Parameters |
Phrap Advanced Defaults |
|||
|
Pairwise Alignments |
||||
|
"Insertion gap penalty" |
-100L |
0L |
InsGapExt |
-3; |
|
"Deletion gap penalty" |
-100L |
0L |
DelGapExt |
-3; |
|
Use Raw SWAT scores |
Raw |
false; |
||
|
Banded Search |
||||
|
MaxGroupSize |
20; |
|||
|
"Maximum group size" |
0L |
1000L |
WordRaw |
false; |
|
"Half bandwidth" |
-0L |
1000L |
Bandwidth |
14; |
|
Input |
||||
|
"Default quality values" |
0L |
99L |
DefaultQual |
15; |
|
"Trim start" |
0L |
1000L |
TrimStart |
0; |
|
Assembly |
||||
|
Bypass level |
Bypasslevel |
1; |
||
|
Revise Greedy |
ReviseGreedy |
false; |
||
|
Shatter Greedy |
ShatterGreedy |
false; |
||
|
Pre-assemble groups |
PreAssemble |
false; |
||
|
Ignore high Qual discrepancies |
ForceHigh |
false; |
||
|
Phrap Miscellaneous Parameters |
Phrap Miscellaneous Defaults |
|||
|
Miscellaneous |
||||
|
"Maximum subclone size" |
1000L |
10000000L |
MaxSubcloneSize |
5000; |
|
"Index word size" |
1L |
20L |
Indexwordsize |
10; |
|
Retain Duplicate reads |
RetainDuplicates |
false; |
||
|
Trimming |
||||
|
"Trim penalty" |
-100L |
0L |
TrimPenalty |
-2; |
|
"Minimum trim score" |
0L |
1000L |
TrimScore |
20; |
|
"High quality threshold" |
0L |
99L |
TrimQual |
13; |
|
Confirmation |
||||
|
"Minimum segment size" |
1L |
1000L |
ConfirmLength |
8; |
|
"Trim segment ends" |
0L |
100L |
ConfirmTrim |
1; |
|
"Penalty" |
-100L |
0L |
ConfirmPenalty |
-5; |
|
"Minimum score" |
1L |
1000L |
ConfirmScore |
30; |