About HQTB

The high-quality template based (HTQB) workflow curates the model starting from the annotated genome of your strain of interest and an already curated, ideally very high-quality template model of a closely related strain (species) and additional database information.

This type of workflow aims to build upon already existing knowledge to speed up model curation and minimize the need to perform steps again that have already been done in a similar context.

Overview of the HQTB Workflow

The following image shows an overrview of the steps of the workflow:

The workflow consists of five main steps:

• Step 1: Bidirectional BLAST
• Step 2: Draft Model Generation

• Step 3: Model Refinement
  Refine the previously generated draft model to make the model more complete and strain-specific. In other words, fitting it more closely to the input genome.

  • Part 1: Extension

  • Part 2: Clean-up

  • Part 3: Annotation

  • Part 4: Smoothing

• Step 4: Validation
• Step 5: Analysis

The wrapper function allows the curation of multiple models sequentially using the same boudary parameters.

Hint

Many of the steps of the workflow can be fine tuned and turned off/on. Check the configuration file for a full list of all parameters.

Note

All steps of the workflow can be run separatly via the command line or the Python integration (see Run the HQTB Workflow).

All accessible functions are listed in the Contents of SPECIMEN section.