FAKtory is a software environment for supporting DNA sequencing projects. FAKtory runs on machines configured with the UNIX operating system. It is called FAKtory because it employs our FAKII Fragment Assembly Kernel that is a C-library of routines incorporating our best algorithms for solving the shotgun assembly problem. FAKtory is highly configurable and can perform fragment clipping, prescreening, and tagging functions, shotgun assembly with or without constraints, and sequence finishing. An extensible input/output mechanism permits FAKtory to be inserted into any informatics environment.

This document provides an overview of the concepts and functioning of FAKtory.

1. Customization & Preferences
2. Projects Files
3. Fragment Database
4. Fragments Panel
5. The Pipeline
6. Input/Output
7. Prescreeners
8. Constraints
9. Layout Edit Panel
10. Finishing Panel

• FAKtory can be configured with a very large range of options, making it flexible. The resulting complexity is shielded from end users by a default scheme which permits a master user to establish a lab-customized configuration that all end users see by default.

• FAKtory has been designed to permit co-operative work on a given sequencing project.

• FAKtory provides a general-purpose fragment database: the type and format of the data kept for each sequencing reaction is configurable, one may control the vocabularies for given fields and establish default values for them, one may sort and view records on any combination of fields, and one may select sets of fragment records using an SQL-like query mechanism that supports string searches.

• FAKtory provides a fragment pipeline which is a configurable sequence of processing stages through which fragments must pass. There are stages for input, overlap detection, assembly, and prescreening activities such as vector removal, poor-data trimming, and Alu tagging. The FAKtory supports modes of processing from fully automatic to completely manual, and further provides a review mechanism for handling processing anomalies.

• FAKtory uses the ideas of input and output filters to make it extensible, e.g., handling an unlimited range of input formats and linking to an unlimited range of post-analysis programs.

• The FAKtory prescreener stages employ a very general framework that permits users to develop sophisticated criteria for clipping or tagging data.

• FAKtory provides a mechanism that allows for the automatic association of constraints for pairs of fragments based on naming conventions. The constraints can be any combination of overlap, orientation, and distance constraints as realized by the FAK II assembly kernel.

• FAKtory supports the idea of an assembly scratchpad where one can manipulate and interact with a set of possible alternate solutions to a given data set.

• The FAKtory finisher automatically keeps track of edited regions of a multi-alignment, organizing the task of editing the penultimate solution.