Sperm whale radseq population structure

This repository contains scripts to analyze RADseq data from 73 sperm whale samples across the Gulf of Mexico and Atlantic.

Raw data can be found at NCBI bioproject PRJNA1189584

All scripts are found in the scripts directory and their function is described below.

For questions contact Reid Brennan: reid.brennan@noaa.gov or reid.brennan@gmail.com

Filtering

1. Fastqc raw files: fastqc.nf
2. rename:
   • rename.sh SNP052_sperm_whale_plateB_75_indexes_HS100_437.txt
3. Trim with fastp:
   • nextflow run fastp.nf --fastq "raw_data/*.R1.fq.gz"
4. Fastqc trimmed files:
   • nextflow run fastqc.nf --input_dir ./analysis/trimmed_files --outdir ./analysis/fastqc_post_trim
5. Align with bwa mem2:
   • nextflow run bwa.nf -c nextflow.config -profile bwamem2
6. calculate alignment stats:
   • nextflow run bam_stats.nf -c nextflow.config -profile bamstats, outputs: count.aligned.txt
7. Call variants with freebayes:
   • freebayes_parallel.sh
8. Filter SNPs:
   • filter.1.sh: First pass depth, missingness, bialleleic and snps only, depth.
   • filter.2.sh: Remove Pmac075, truncated file. max missing 0.7, maf 0.05, min mean depth 10x, allelic balance
   • filter.R: requires HDplot.R. Max depth, HDplot for paralogs
   • filter.3.sh: remove sites found in filter.R

filtered.final.vcf.gz: 4441 snps

Analysis

• PCA with all individuals:
  • plink_pca.sh
  • plot results: pca.R
    • note that this includes related individuals
• Relatedness
  • ngsrelate.sh
  • relatedness.R
  • filter_related.sh
• PCA unrelated individuals only
  • plink_unrelated.R
  • pca_unrelated.R
• Admixture
  • admixture.sh
  • admixture.R
• DAPC
  • dapc.R
• genetic diversity
  • pi:
    • Call allsites for accurate pi estimations: freebayes_allSites.sh
    • filter this vcf: filter.allsites.1.sh
    • calculate pi with Pixy: pixy.sh
  • heterozygosity
    • stacks_populations.sh
    • diversity.R
  • diversity.R to do analyses, make plots, etc.
  • Fig3.R also combines plots, calculates Fst
• Effective population size
  • Ne_estimations.md

Mitochondrial analysis - mitotyping.R

Figures:

• Fig. 1: map.R
• Fig. 2: relatedness.R
• Fig. 3: Fig3.R
• Fig. 4: diversity.R
• Fig. 5: mitotyping.R. Note that this figure required popart and was manually put together.

Supplemental figs:

• Fig. S1: relatedness.R
• Fig. S2: pca_unrelated.R
• Fig. S3: admixture.R
• Fig. S4: dapc.R
• Fig. S5: dapc.R
• Fig. S6: pca_unrelated.R
• Fig. S7: admixture.R

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