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Enter Assembly into Gap4

Filename
enter_assembly.p4m

Description
This module is used to enter assemblies into Gap4 which have been generated externally to Gap4 (ie everything 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:
Option: Gap4 database name
Option: Gap4 database version
The name of version of the database to assemble in.

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 any warnings.

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 better to use difference clipping instead.

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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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_31.html