Genomic analysis of adaptive immune loci in the primate T2T project

The repository contains data and scripts for analysis of immunoglobulin (IG) and T-cell receptor (TR) loci in genomes of four great ape species (bonobo, gorilla, Sumatran orangutan, and Bornean orangutan) assembled by the Primate T2T project.

Data

• data_primate_igtrloci_locus_config.csv: positions of IG/TR loci in genome assemblies of four great species.
• data_primate_igtrloci_fasta/: FASTA files with haplotype-resolved sequences of IG/TR loci in assemblies of four great species.
• data_primate_gene_positions/: positions of germline IG/TR genes across four great species.
• data_human_t2t_gene_positions/: positions of germline IG/TR genes in the human T2T assembly.
• data_locus_alignments/: positions of long non-overlapping alignment blocks computed across pairs of IG/TR loci.
• data_SV_block_positions/: positions of structural variation blocks computed within IG/TR loci.
• configs/: config files containing paths to all data files for each of the loci as well as information about locus lengths and orientations in the assembly.

Code

Dependencies:

• BioPython.
• pyGenomeViz, v.0.4.4.

Visualization of genomic diagrams

python visualize_genome_diagram.py locus_config.txt output_fname.png

E.g.: python visualize_genome_diagram.py configs/config_IGH.txt IGH_diagram.png

Visualization of gene count plots

python visualize_gene_counts.py locus_config.txt output_fname.png

E.g.: python visualize_gene_counts.py configs/config_IGH.txt IGH_gene_counts.png

Citation

Yoo D, et al. Complete sequencing of ape genomes. BioRxiv, 2024