Insect_GC_content

Code repository for all scripts used to collect data, perform statistics and create figures for the paper "GC content across insect genomes: phylogenetic patterns, causes and consequences"

Contents

/01 - Global/

00 - Intro/

1) GC_totals_eukaryotes.py

Script used to calculate GC content totals for different Animal subgroups using data from NCBI (https://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt)

01-GenomeGC/

1) get_genomes.py 

Script to download genomes from DTOL

2) chrm_number_GC_content.py

Script to calculate GC content per chromosome/scaffold in a genome with a given cutoff size (> 1MB)

3) get_mean_GC.py

Script to calculate mean GC for species when given chromosome data

01-cdsGC/

1) get_genes.py

Script to download cds and protein data from DTOL

2) cds_GCcontent.py

Script to calculate cds GC content per chromosome/scaffold in a genome with a given cutoff size

3) get_mean_GC.py

Script to calculate mean GC for species when given inidivual chromosome data

01-GC3/

NOTE: Scripts here use sinlge copy orthologue ouptus from orthofinder runs

1) orthofinder_GC3.py

Script to calculate aligned GC3 for orthofinder orthogroups given cds primary transcripts, as well as other gene metrics

2) get_mean_species_GC3.py

Script to calculate mean GC3 for each species

figure-1.1/

1) species_GC_comaprison.R

R script used to create Figure 1

/02 - Phylogeny/

1) phylogeny_plots.R

Script to produce Figure 1

/03 - Size/

1) size_plots.R

Script to produce Figure 3, using outputs from 01-GenomeGC

/04 - Telomere/

1) get_telomere_plot.py

Script to calculate distance from telomere for each single copy orthologue and it's corresponding GC3 %

2a) figure-4.1/chromosome_plots.R
2b) figure-4.1/telomere_distance.R

Scripts to produce Figure 4

/05 - Bombylius/

1) get_sneath_index.py

Script to calculate sneath value index. This script uses function from get_genetrees.py so must be in the same dir as that script:

2) get_genetrees.py 

Provides functionality to get_sneath_index.py, doesn't need to be run

/Data/

All data used in this paper provided:

• all_output_data.xlsx

Order of tabs:

genome IDs; genome GC; CDS GC; SCO GC3; species tree files; chromosome size GC; regressions between chromosome size and GC; SCO gene identification numbers, chromosomal location and GC3; average distances from telomeres; codon usage data; Sneath values

Installation

  git clone https://github.com/RiccardoKyriacou/Insect_GC_content