Bioinformatics, Genomics, population genomics
Repositories
PMuchina/BSF_genomics_pipeline
Analysis scripts, pipelines, and data processing code for the study “Human activity shapes the current global distribution of wild and captive black soldier flies (Hermetia illucens)”. This repository includes workflows for WGS data processing, variant filtering, genotype imputation, and population genomic analyses
PMuchina/BSF-Reference-Panel
Establishing a Reference Genome Panel and Evaluating Imputation Strategies for Low-Coverage Sequencing in Black Soldier Fly (Hermetia illucens)
PMuchina/Meta-analysis
Meta_analysis
PMuchina/pmuchina.github.io
PMuchina/ld_population_history_demo
PMuchina/Buffalo_PopGenomics
Scripts for processing and analysing resequencing data, as well as R scripts for producing figures from some of the results for the manuscript: de Jager, D. et al. High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes. Sci. Rep. 11, 4540, doi:10.1038/s41598-021-83823-8 (2021).
PMuchina/seqAfrica_bushpigs
Git repository for the African pig project at the University of Copenhagen.
PMuchina/Population_genomics_pipline
PMuchina/PhysaliaPopGen
PMuchina/imputation_accuracy_calculator
PMuchina/lcwgs-guide-tutorial
PMuchina/physalia-lcwgs
Files for the the Physalia course on Population genomic inference from low-coverage whole-genome sequencing data, Oct 10-13, 2022
PMuchina/dDocent
a bash pipeline for RAD sequencing
PMuchina/presentations
Presentations from the course
PMuchina/My_scripts
PMuchina/LoCSI-for-non-model-species
PMuchina/population_genomics
Scripts
PMuchina/ngsTools
Programs to analyse NGS data for population genetics purposes
PMuchina/VCF2Fasta
PMuchina/Speciation-scripts
Scripts for analysis used during the course
PMuchina/Intro2PopGenomics
Leroy & Rougemont - “learning-by-doing” introduction to population genomics - scripts
PMuchina/whole-genome-reseq
Scripts for the analysis of low-coverage whole genome resequencing data
PMuchina/vcfR
Tools to work with variant call format files
PMuchina/Python4Bioinformatics2019
Updated materials for MSc Bioinformatics for Pwani University
PMuchina/alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
PMuchina/Long-read-assembler-comparison
Benchmarking of long-read assembly tools for bacterial whole genomes
PMuchina/Learn_Bioinformatics
PMuchina/Bioinformatics-training-collection
A collection of resources for learning about tools and programming languages related to Bioinformatics
PMuchina/bioinformatics
:microscope: Path to a free self-taught education in Bioinformatics!