CONGA 0.0.2

Combined Open and Narrow searches via Group Analysis

CONGA is a tool for discovering peptides in mass spectrometry data with rigourous FDR control. It is designed to allow for unexpected post-translational modifications as well as chimeric spectra. Open Group-walk takes three inputs: (1) the set of top-scoring PSMs from a traditional, narrow-window search against a concatenated target-decoy database, (2) the set of top-k PSMs (or fewer if less than k PSMs exist) from an open search, again against a concatenated target-decoy database, and (3) the pairs of target and decoy peptide sequences from the database. Given this, Open Group-walk will return a discovery list of peptides.

Documentation

You can find documentation on how to use CONGA over on readtheddocs. Alternatively you can find the same documentation under docs/pages in this respository.

Paper

A link to the biorXiv paper will eventually go here.

Installation

To install, first create a virtual environment using conda:

conda create --name conga_env python=3.9

Then activate this virtual environment:

conda activate conga_env

Next download the latest release from Github. Use pip to install CONGA:

pip install Downloads/CONGA-x.x.x.tar.gz

If the CONGA folder is not in the Downloads folder, you will have to specify the path to CONGA:

pip install path/to/CONGA-x.x.x.tar.gz

Please see the documentation, specifically the tutorial, on how to run CONGA.

Releasing

Releases are published automatically when a tag is pushed to GitHub.

# Set next version number
export RELEASE=x.x.x

# Create tags
git commit --allow-empty -m "Release $RELEASE"
git tag -a $RELEASE -m "Version $RELEASE"

# Push
git push upstream --tags