This repository contains all of the code relevant to my investigation into the large structural polymorphism found on the right arm of chromosome 5 of the Daphnia magna genome. There are several modules:

Module 1: Chromosome 5 synteny analysis

This module performs a genome synteny analysis across a set of reference Daphnia genome assemblies using the GENESPACE software, and then plots the results for chromosome 5 using custom R scripts.

Component script files:

• genespace.md (contains multiple sub-scripts)
• repeat_modeling.sh
• protein_extract.sh

Required input files:

• A set of reference genome assemblies
• An index file ("genome_index.txt") of the genome assembly file names

Optional input files:

• Pre-trained gene models or RNA-seq data for Augustus gene prediction. The model used in this analysis is named "Dmagna_iso"

Module 2: Chromosome 5 dotplot alignment

This module extracts all candidate contigs from individual genome assembly which appear to belong to chromosome 5, and concatenates them together into individual chromosome 5 FASTA files. All pairwise combinations are then reciprocally aligned together using an interactive DGENIES session (based on MiniMap). The alignment files are then visualized as a matrix of pairwise alignments using custom R code.

Component script files:

• chromosome_5_scaffolding.md (contains multiple sub-scripts)
• dotplot_matrix_main.R
• dotplot_matrix_utils.R

Required input files:

• A set of reference genome assemblies from which to extract the chromosome 5 contigs

• DGenies output folders for each pairwise chromosome 5 alignment

Module 3: Linkage Disequilibrium (LD) calculations

This module calculates LD across chromosome 5 using a previously created VCF file from 258 D. magna short-reads mapped against a single reference genome.

Component script files:

• linkage_disequilibrium.md (contains multiple sub-scripts)

Required input files:

• An input VCF file "merged_daphnia_filtered.vcf"

Module 4: GC bias calculations

This module calculates GC content across the right arm of chromosome 5 for multiple genome assemblies using a custom perl script and then plots the results using a custom R script.

Component script files:

• GC_calculations.md (contains multiple sub-scripts)

Required input files:

• An input VCF file "merged_daphnia_filtered.vcf"

Module 5: HDH orthology analysis for Lake Aegelsee

This module performs a gene orthology analysis on the three HDH haplotypes which were observed in Lake Aegelsee based on the genome annotation files which were previously created by AUGUSTUS in the GENESCAPE module.

Component script files:

• orthology_analysis.md (contains multiple sub-scripts)

Required input files:

• Genome annotation files from Augustus (one for each genome)
  • "t2_17_3_4i_13.gff3"
  • "CH_434-inb3-a-1.gff3"
  • "t1_10_3_2.gff3"
• Gene model predictions from Augustus (one for each genome)
  • "t2_17_3_4i_13_functional.tsv"
  • "CH_434-inb3-a-1_functional.tsv"
  • "t1_10_3_2_functional.tsv"
• Orthogroup master list from Augustus
  • "Orthogroups.tsv"

Module 6: HDH coordinate BLAST