GenErode pipeline

<img src="docs/source/img/logga_viridis2.png" alt="logo" width="25%"/>

GitHub repository for GenErode, a Snakemake workflow for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.

Documentation

The full pipeline documentation can be found on the repository wiki.

Citation

If you've used GenErode to produce results, please cite our paper:

Kutschera VE, Kierczak M, van der Valk T, von Seth J, Dussex N, Lord E, Dehasque M, Stanton DWG, Emami P, Nystedt B, Dalén L, Díez-del-Molino D (2022) GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. BMC Bioinformatics 23, 228 https://doi.org/10.1186/s12859-022-04757-0

Pipeline overview

<img src="docs/source/img/figure_1_generode_pipeline_v7.png" alt="processing" width="75%"/>

Figure 1: Overview of the GenErode pipeline data processing tracks. Input and output files formats, dependencies between steps, and main software used are shown. Optional steps are highlighted in red.

<img src="docs/source/img/figure_2_generode_pipeline_v7.png" alt="analysis" width="75%"/>

Figure 2: Overview of the GenErode pipeline data analysis tracks and final reports. Input file formats and main software used are shown.

Licence information

GenErode pipeline

Copyright (C) 2022 Verena Kutschera

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Logo: Jonas Söderberg