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createACE=integer (default=0)
If non-zero, create an ACE file for the scaffolds.
doToggle=integer (default=0)
If non-zero, at the end of a successful assembly, search for placed surrogates and toggle them to be unique unitigs, then re-run the assembly starting from scaffolder.
1 하면 됨
unitigger=bog
This determines which unitig module to invoke. This flag, whether issued on the command-line or in a spec file, will override the defaults.
The default is utg, but the default behavior is influenced by flags in the input FRG files.
For instance, BOG will run by default if the input FRG file contains even one LIB message with the attribute "forceBOGunitigger=1".
Celera Assembler offers two unitig module but the pipeline can only run one. The original unitigger (UTG) was designed for Sanger capillary data.
The best overlap graph unitigger (BOG) was designed for 454 pyrosequencing data.
More generally, BOG is best for higher coverage and variable-length reads. BOG is faster than UTG.
Since the BOG module benefits from continued development and maintenance, it is probably best for all data types.
doToggle=1
If non-zero, at the end of a successful assembly, search for placed surrogates and toggle them to be unique unitigs, then re-run the assembly starting from scaffolder.
clossurePlacement=1
Options for placing closure reads using the constraints.
0. Place at the first location found.
1. Place at the best location (indicated by most satisfied constraints).
2. Place at multiple locations as long as the closure read/unitig in question is not unique.
Currently recommended settings are closureOverlaps=0 and closurePlacement=2.
