This module is used to enter assemblies into gap4 which have been generated
externally to gap4 (ie all assembly engines except "Gap4 shotgun assembly"). This is
achieved by using the gap4 "Directed Assembly" function. The assembly is read
from the fofn.assembly directory, where fofn is the filename prefix
listed in the "Files to Process" panel.
- Option: Gap4 database name
- Option: Gap4 database version
The name and version of the database to assemble into.
- Option: Create new database
This is a toggle to define whether the specified gap4 database should be
created or appended to. Be warned that at present creating a new database
will overwrite existing one of the same name, in the same directory, without
- Option: Post-assembly quality clipping
- Option: Lowest (average) quality to use
This can be used to direct gap4 to run the "Quality Clip" function after
entering the assembly. This performs quality clipping by identifying segments
where the average quality is below a particular threshold. This should only be
necessary if quality clipping was not performed earlier (eg because Phrap was
used for assembly), and even then it is usually better to use difference
- Option: Post-assembly difference clipping
This can be used to direct gap4 to run the "Difference Clip" function after
entering the assembly. This identifies ends of readings where the alignment
between readings and consensus is bad and marks these ends as hidden data. This
is primarily designed for use after the Phrap assembly engine, which sometimes
leaves poorly aligned end fragments.
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Last generated on 22 October 2002.