.. Open Group-walk documentation master file, created by
   sphinx-quickstart on Tue Oct  4 15:20:43 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to CONGA's documentation!
===========================================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   pages/output_files
   pages/parameters
   pages/tutorial_example
   pages/limelight

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

CONGA is a tool for discovering peptides in mass-spectrometry data with theoretical FDR control. It requires three inputs: (1) the set of top-1 PSMs per spectrum using a narrow-window search against a concatenated target-decoy database, (2) the set of top k PSMs (or less if fewer than k PSMs exist for a given spectrum) using an open search, again against a concatenated target-decoy database, and (3) the paired list of target and decoy peptide sequences from the database. Ideally, an additional option is set which specifies the isolation window used. Given this, CONGA will return a discovery list of peptides. CONGA is able to make simultaneous discoveries from both open- and narrow-search files, detect unaccounted for post-translational modifications of the sample peptides, and detect peptides generated by chimeric experimental spectra.

Links
=====
* Source code: https://github.com/freejstone/CONGA
* Paper: To be added
* :ref:`search`