IDEELResearch/PmPopGen

Code used for analysis of African Plasmodium malariae whole genomes derived from hybrid capture enrichment. # PmPopGen This repository contains code used to process and analyze 81 Plasmodium malariae genomes generated via hybrid capture sequencing. The original data files are available via SRA (BioProject ID PRJNA1157442). Shell scripts are used to process sequence read files and are optimized for SLURM sbatch submission. While it is possible to adapt them to run on a Unix desktop, it will take much longer and require a large quantity of memory and storage space. Initial processing using these shell scripts is expected to take up to a week on a high-performance computing cluster. In order to run the subsequent analysis, you will need a working installation of R and RStudio. Code was optimized to run in R 4.2.2 and RStudio 2022.07.2. Individual R packages are detailed within each respective script. Shell scripts rely on functioning installations of trim_galore, BBMap, bwa-mem2, GATK4, bcftools, vcftools, Tandem Repeats Finder, bedtools, python3, dadi-cli, donni, ADMIXTURE, PLINK v1.9, and RAxML Next Generation. The following scripts are intended to be run in the order given: 1. Pm_trim_individual_scripts.sh: trims sequencing adapters from fastq files 2. Pm_bbsplit.sh: competitively aligns reads across multiple reference genomes 3. Pm_bwa_individual.sh: select reads best aligned to the Pm reference genome after competitive alignment 4. Pm_Picard.sh: adds readgroup information to Pm-aligned bam files 5. Pm_HC_generate_gVCF.sh: generate gVCF files of variants across Pm genome for each sample 6. Pm_HC_genotype_gVCFs.sh: genotypes individual gVCF files across entire sample pool, yielding vcf file showing variant sites 7. Pm_filtering_determination.R: titrate quality filtering thresholds for raw variant output from unfiltered vcf file 8. Pm_VariantFiltration.sh: applies hard quality filtering and missingness thresholds to VCF file, limits to SNPs, and excludes hypervariable regions 9. COI_Pm_coiaf.R: estimates complexity of infection for each sample using COIAF 10. Pf_s …