[[workflow]]
Workflow
--------

As a preprocessing step IGoR first needs to align the genomic templates
to the read (`-align`, see detailed commands in the <<alignments, Alignments commands section>>) before exploring all putative recombination
scenarios for this read. After aligning IGoR can be used to infer a
recombination model (`-infer`, see the <<inference-and-evaluation, Inference/Evaluation section>>), evaluate sequences statistics
(`-evaluate`) using an already inferred model. Synthetic sequences can
be generated from a learned model (as one supplied by IGoR, or one
inferred de novo through the `-infer` command) with the `-generate` (see the <<sequence-generation-commands, Sequence generation section>>)
command.

include::workflow/supplied_models.adoc[]

include::workflow/model_validity.adoc[]
