Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.

pipeline: from sra, bed, vcf to plink

This repository contains code related to a conservation genomics project focused on the king rail, a threatened marsh bird.

PalaeoKin is a lightweight ancient-DNA pipeline for estimating pairwise relatedness from mapped BAMs at low/uneven coverage. It wraps ANGSD + NgsRelate (KING-robust kinship, R0/R1) and samtools, producing a clear summary plus PDF/SVG QC plots, with optional downsampling and allele-balance/mixture diagnostics.