Wildlife Genomics4@Pwani: Population Genomics Workshop for Pwani University

This repository contains datasets for learning population genomics. These are 150 bp paired-end whole-genome sequences of lions generated on the Illumina sequencing platform. This is designed for the wildlife population genomics workshop held at Pwani University. The tutorial regarding the dataset is described here: https://poodl-ces.github.io/Wildlife_genomics_4.io

The FASTQ files in the sub_samples.tar.gz archive are a random subset of 100,000 reads of the raw FASTQ files that were submitted in the SRA database and/or utilized by the authors of the following publications:

- Cho, Y. S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., ... & Bhak, J. (2013). The tiger genome and comparative analysis with lion and snow leopard genomes. Nature Communications, 4(1), 2433.
- De Manuel, M., Barnett, R., Sandoval-Velasco, M., Yamaguchi, N., Garrett Vieira, F., Zepeda Mendoza, M. L., ... & Gilbert, M. T. P. (2020). The evolutionary history of extinct and living lions. Proceedings of the National Academy of Sciences, 117(20), 10927-10934.
- Barazandeh, M., Kriti, D., Fickel, J., & Nislow, C. (2024). The Addis Ababa Lions: whole-genome sequencing of a rare and precious population. Genome Biology and Evolution, 16(2), evae021.
- Bertola, L. D., Vermaat, M., Lesilau, F., Chege, M., Tumenta, P. N., Sogbohossou, E. A., ... & Vrieling, K. (2022). Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo). BMC Genomics, 23(1), 321.

The SRA accessions that were extracted and subsetted can be found in the file SRA_metadata.csv. Effort was made to obtain only modern (not museum or historical DNA) sequences to simplify the workflow for a beginner-level workshop.

The repo also contains the lion's reference genome and its BWA index files. The reference genome for Panthera leo used is the one with accession number GCF_018350215.1.

Additionally, the repo contains variants that were called using the Strelka2 germline workflow. The variants are called for the 239 Mb long scaffold with NCBI accession NC_056679.1 in the lion reference genome assembly.