Introduction
============

LENS
____

Landscape of Effective Neoantigen Software (LENS) is a tumor antigen
discovery workflow capable of identifying potential therapeutic cancer
immunotherapy targets from seven antigen sources. More information on LENS can
be found in the `LENS publication <https://academic.oup.com/bioinformatics/article/39/6/btad322/7162685>`_.

LENS predicts peptide-MHCs (pMHCs) from seven antigen sources:

- Somatic Nucleotide Variants (SNVs)
- Somatic Insertion and Deletion Variants (InDels)
- Splice Variants
- Fusion Events
- Endogenous Retroviruses (ERVs)
- Viruses
- Cancer-testis Antigens (CTAs)

.. note::

   Ready to get started? See :doc:`quick_start` to install RAFT and run a
   demonstration.

Sample Prerequisites
____________________

LENS can be run on multiple patients simultaneously and there are benefits to
running multiple patients (such as shared tumor splice variant detection with
``SNAF`` and improved CNA detection with ``CNVKit``), but only one patient worth
of samples is required.

It is strongly recommended to run LENS with the following sample types (per
patient) for the best experience:

- DNA tumor
- DNA normal
- RNA tumor

Alternatively, the following sample types (per patient) can be used to get
fusion, splice, ERV, viral, and CTA pMHCs:

- RNA tumor

Additionally, users should provide a tissue-matched normal RNA sample (e.g.
GTEx or `Fagerberg et al., 2014 <https://www.mcponline.org/article/S1535-9476(20)34633-8/fulltext>`_).

More information on running multiple sample sets per patient (e.g. primary vs.
metastasis, pre-treatment vs. post-treatment, multiple timepoints, etc.) can be
found in the :doc:`preparing_your_samples` section.

.. image::
   patient_names_and_runs.png
   :width: 675