awesome-genomic-skills Public

A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc

fungal_genome_assemblies Public

Scripts used to download and analyse fungal genomes assemblies from NCBI and JGI MycoCosm

KaryoScope Public

KaryoScope: rapid, alignment-free sequence annotation for the pangenome era

tax_amr Public

pangenome Public

nextflow-pipeline Public

aakomp Public

Draft genome completeness assessment using k-mer hash based approach

bravo_project Public

Transcriptome analysis of oilseed rape genotypes

TomatoT2Tsuperpangenome Public

Codes for tomato T2T super pangenome

Yedomon Public

code for github profile

R-for-geographic-map-Session-1 Public

R for a geographic map

Pan-genome_wheat4 Public

Graph-based pangenome construction of tetraploid wheat

Capsule Public

Comprehensive Reproducibility Framework for R and Bioinformatics Workflows

multiOmics-integration Public

Potato ‘omics data analysis pipelines

PlantGenomicsGuide Public

Instructions for all major step in a plant genome sequencing project

Crip_PopulationHistory_Centromere_2025 Public

This is the repository for the manuscript Pettrich et al. 2025. High quality genome assembly of Chironomus riparius and its population history in European populations.

multi-omics-diablo-pipeline Public

Code for integrating transcriptomics, methylation, and proteomics data using DIABLO

dogme Public

A nextflow pipeline for calling modifications in nanopore reads.

GCI Public

A program for assessing the T2T genome continuity

colora Public

A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitochondrion and/or chloroplast). It automatically assesses the q...

run_mcscanx Public

HiGenAA Public

Wild-rice-Pangenome-Project Public

This repository contains all codes and scripts used in the Wild Rice Pangenome Project. The project aims to provide a comprehensive analysis of a pangenome reference of wild and cultivated rice. Be...

cottonRef_ZM113 Public

Scripts used to analyze the T2T reference genome of G. hirsutum cv. ZM113

multiomics-data-analysis-and-integration-training Public

Citrus_Pangenes Public

WGD_Tracker Public

Vigna-pan-genome Public

De novo assembled 11 representative Vigna accessions from 580 collected accessions, and performed pan-genome and population genomics studies of Vigna.

Pan_Bulbosum Public

Code for Article "A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum"

GBioS_Training_Genomics_Plant_Breeding_2024 Public