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European Green Woodpecker Genome Assembly

Overview

This repository contains scripts and tools for the assembly and analysis of the genome of the European Green Woodpecker (Picus viridis). The assembly process involves various steps, including chromosome naming, visualization using Circos, calculation of pi diversity, population genetics statistics, and analysis of the site frequency spectrum (SFS).

Repository Structure

  • Circos: This directory contains scripts and files related to the visualization of the genome using Circos.

    • circos_picus_colaptes.R: Circos script for visualizing the genome with related species (Colaptes auratus).
    • circos_picus_gallus.R: Circos script for visualizing the genome with the reference model organism, the Chicken (Gallus gallus).
    • pviridis_chromosomes_names.csv: CSV file containing chromosome names for Picus viridis.
    • rename_picus_chr_v2.py: Python script for renaming Picus viridis chromosomes.
    • Rename_picus_contigs.ipynb: Jupyter notebook for renaming Picus viridis contigs.
    • rename_tablev2.csv: CSV file containing renaming information.
    • run_mummer.sh: Shell script for running MUMmer, a system for aligning whole genome sequences.

  • pi_diversity.sh: Shell script for calculating pi diversity, a measure of nucleotide diversity.

  • popgen_stats_picus.R: R script for computing population genetics statistics.

  • SFS: This directory contains scripts related to the analysis of the site frequency spectrum (SFS).

    • customgraphics.py: Python script for custom graphics related to SFS.
    • SFS_picus.py: Python script for computing the SFS for Picus viridis.
    • sfs_tools.py: Python script containing tools for SFS analysis.

Components description

  1. Genome Comparison:

    • Execute run_mummer.sh for genome comparison using MUMmer. Used as an input for sytneny analysis and Circos plotting.

  2. Chromosome Naming and Visualization:

    • Use rename_picus_chr_v2.py and Rename_picus_contigs.ipynb for renaming chromosomes and contigs accordingly to the genome of Gallus gallus.
    • Run Circos scripts (circos_picus_colaptes.R and circos_picus_gallus.R) for visualization.

  3. Population Genetics Analysis:

    • Run pi_diversity.sh for calculating Watterson's Pi diversity using vcftools.
    • Execute popgen_stats_picus.R for additional population genetics statistics.

  4. Site Frequency Spectrum Analysis:

    • Utilize scripts in the SFS directory for analyzing the site frequency spectrum.

License

This project is licensed under the MIT License - see the LICENSE file for details.