The Sage pipeline has been created to process SAGE data, which requires a different approach than standard NGS data.
### Modules and Tools
# Tools for this pipeline
This pipeline uses the following modules and tools:
*[Flexiprep](flexiprep.md)
*[Mapping](mapping.md)
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*[SageCreateTagCounts](../tools/sagetools.md)
# Example
## Configuration
Note that one should first create the appropriate [configs](../general/config.md).
To get the help menu:
## Running Sage
As with other pipelines, you can run the Sage pipeline by invoking the `pipeline` subcommand. There is also a general help available which can be invoked using the `-h` flag:
Below is an example of the output files that you will get after running Sage. Here, we have two samples (`1A` and `1B`) and each sample has two libraries (`run_1` and `run_2`).