.. _besca-standard-pipeline:

=======================
besca standard pipeline
=======================



Besca standard worklow offers a standardized series of steps from raw-data to filtered one in order to start the annotation processes.




Besca is distributed with such workflow available as a notebook:
https://github.com/bedapub/besca/blob/master/workbooks/standard_workflow_besca2.ipynb


The differents individuals steps are described in the tutorial:
:doc:`data processing <tutorials/notebook1_data_processing_pbmc3k>` 



And different examples are available in the publication results repository:

`PBMC3K standard workflow <https://github.com/bedapub/besca_publication_results/blob/master/hematopoietic/pbmc3k/standard_workflow_besca2-Raw.ipynb>`_

`Lee 2020 Intestine standard workflow <https://github.com/bedapub/besca_publication_results/blob/master/intestine/Lee2020/standard_workflow_besca2.1_sc145_bescapub.ipynb>`_

`Granja 2019 hematopoietic standard workflow <https://github.com/bedapub/besca_publication_results/blob/master/hematopoietic/Granja2019/standard_workflow_besca2.0_updated.ipynb>`_