Welcome to CFEIntact’s documentation!

CFEIntact is BCCfE’s version of HIVIntact – a python-based program for characterisation of genomic defects in NFL HIV-1 sequences, allowing putative intact genomes to be identified in-silico.

CFEIntact stands out from other applications in its ability to seamlessly integrate into existing sequence-analysis pipelines. This makes it an ideal tool for analyzing large next-generation sequencing datasets. By incorporating CFEIntact into your workflow, you can:

• Identify intact genomes: CFEIntact utilizes algorithms for identification of intact genomes within NFL HIV-1 sequences.
• Enhance efficiency: By integrating CFEIntact into your existing sequence-analysis pipelines, you can streamline your workflow and save time.
• Scale up: CFEIntact is designed to handle large next-generation sequencing datasets, allowing you to analyze vast amounts of data with ease.

Contents

This documentation website contains the following sections:

• Installation: Instructions on how to install the CFEIntact executable.
• Running CFEIntact: Instructions on how to run the CFEIntact program.
• Inputs and Outputs: Learn about the supported input formats and the output generated by CFEIntact.
• Workflow: Understand the step-by-step logic of CFEIntact.
• Tolerance limits: Lists values that CFEIntact uses when checking things like ORF’s lengths and their genetic distances.
• Project background: Development history of CFEIntact.