Enter Assembly into Gap4

Description

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 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 usually 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.