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bcf-reader

BCF reader in pure Rust (https://docs.rs/bcf_reader/latest/bcf_reader/)

bmibdcaller_empirical

a Nextflow pipeline to benchmark IBD callers with empirical data by comparing IBD-based estimates with expected patterns of Plasmodium falciparum populations

bmibdcaller_simulations

a Nextflow pipeline to benchmark different IBD detection methods and optimize IBD caller-specific parameters by simulating Plasmodium falciparum-like genomes and using true IBD

ibdutils

A python package to facilitate identity-by-descent-based analysis

ishare

a Rust crate designed to facilitate the analysis of rare-variant sharing and identity-by-descent (IBD) sharing.

msprime

Simulate genealogical trees and genomic sequence data using population genetic models

nextflow-gotchas

A collection of unexpected challenges and learnings with nextflow and nf-core.

polars_python_rust_example

Allow conversion of polars dataframes and series between rust and python (based on https://github.com/pola-rs/polars/tree/master/examples/python_rust_compiled_function)

posseleff_empirical

Nextflow pipeline for analyzing empirical WGS data for the effect of positive selection on IBD-based inference

posseleff_simulations

Nextflow pipeline to assess the impact of positive selection on Identity by Descent (IBD)-based inferences, utilizing population genetic simulations and true IBD inferences.

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

snp_call_nf

Nextflow pipeline for plasmodium SNP calling

testdata

the-elements-of-statistical-learning-python-notebooks

A series of Python Jupyter notebooks that help you better understand "The Elements of Statistical Learning" book

tskibd

Calculate IBD segments from tree sequence using tskit C API

tskit

Analyse, create and manipulate tree sequences.

tskit-rust

Rust bindings for the tskit library

vcfmask

Mask genotype calls when allele depth per sample is too small

wgabed

A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton