FakII Assembly

FakII is not included as part of the Staden Package. It is available from Susan Miller ( susanjo@cs.arizona.edu ).

Description

This module uses the FakII suite of programs to perform shotgun assembly. Output will be placed in the fofn.assembly directory, where fofn is the filename prefix listed in the "Files to Process" panel. The output is in a format suitable for directed assembly within gap4. This can also be performed by using the "Enter Assembly into Gap4" module.

Option: E limit

Option: D limit

Option: O threshold

These parameters control the graph component of FakII, which is used to find the initial overlaps between sequences. For further details, seesection Assembly FAKII.

Option: Auto-generate constraints

When enabled, this uses the reading direction (forward / reverse primers), the template name and the insert size, to produce a file containing data to constrain how the readings may be assembled.

Option: E rate

Option: O threshold

Option: D threshold

These parameters control the assemble component of FakII, which is used for determining the best construction of sequences from the overlap graph.

Option: Assembly number

This allows for non optimum assemblies to be chosen. The optimum assembly is assembly number 1, with the next optimum being number 2, and so on.