alxsimon

local_pcangsd

Local PCA with low-coverage data

quarto-pci

A quarto typst template for Peer Community In (PCI)

assembly_10x

Assembly pipeline for 10X chromium genomes of Mytilus species

Scripts

Useful scripts for my PhD

academics-on-mastodon

A list of various lists consisting of academics on Mastodon

admixcov_data

Variance decomposition analysis of UK and Bohemian human ancient DNA data

admixcov_sims

alxsimon

Chrom-Compare

demes-rs

rust tools for the demes ecosystem

Hybrid_fitness_Fisher_geometric_model

Source code to simulate Fisher's geometric model for two populations in allopatry, used afterwards to study the fitness of hybrids.

insdc-pipeline

SnakeMake pipeline to run BlobTools on public assemblies

local_pca

Methods for examining PCA locally along the genome.

loomio

Loomio is a collaborative decision making tool

Database_Mytilus

Database of Mytilus sp. genotyping data

egrm_legacy

lostruct-py

ms_myt_demo

Manuscript for a demographic inference project on Mytilus.

Mytilus_ref_genomes_paper

nixpkgs

Nix Packages collection & NixOS

nubeamdedup

Removing PCR duplicates for sequencing reads.

pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.

personal_website

Personal website

popgen-notes

Population genetics notes

py-admixcov

Python functions module for the admixture covariance project

pyslim-feedstock

A conda-smithy repository for pyslim.

sgkit-feedstock

A conda-smithy repository for sgkit.

Teaser

A tool to benchmark mappers and different parameters within minutes

tskit

Population-scale genomics

typst-packages

Packages for Typst.