Thiseas C. Lamnidis's repositories
AdmixturePlotter
An R script to generate plots for ADMIXTURE runs, for multiple K values.
Sex.DetERRmine
A python script to calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at specified SNPs.
EigenStratDatabaseTools
A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.
contammix_pipeline
a nextflow pipeline to run Contammix and all the necessary preprocessing for it.
pMMRCalculator
A small python tool to calculate pairwise mismatch rate between all individuals in an EigenStrat dataset.
ContaminateGenotypes
A simple python script to contaminate Eigenstrat genotypes.
minotaur-recipes
Package recipes for processing through the Minotaur workflow
bioconda-recipes
Conda recipes for the bioconda channel.
comp_human_adna_book
This book summarises prepared mini-courses for various computational tools and methods in the field of human archaeogenetic data analysis, with a particular emphasis on population genetics.
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
emu
EM-PCA for Ultra-low Coverage Sequencing Data
ena_scripts
Scripts to assist with data upload to the ena
intro-to-ancient-metagenomics-book
Introduction to Ancient Metagenomics Book
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
nf_core_configs
Config files used to define parameters specific to compute environments at different Institutions
paasta-community.github.io
Website for the PAASTA Community
pyEager
A simple package to read in eager results.
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
test-datasets
Test data to be used for automated testing with the nf-core pipelines