janusx 1.0.25

A Suite of Genotyping Tools for Genome-Wide Association Study and Genomic Selection

JanusX

CLI Guide | Core API Guide | Zea Eureka

Overview

JanusX (Joint Association and Novel Utility for Selection) is a GWAS and genomic selection toolkit that combines:

• Rust-accelerated kernels (PyO3 extension)
• Python analysis modules
• A Rust launcher (jx) for runtime/toolchain management and pipeline orchestration

       _                      __   __
      | |                     \ \ / /
      | | __ _ _ __  _   _ ___ \ V /
  _   | |/ _` | '_ \| | | / __| > <
 | |__| | (_| | | | | |_| \__ \/ . \
  \____/ \__,_|_| |_|\__,_|___/_/ \_\ Tools for GWAS and GS
  ---------------------------------------------------------

Main capabilities:

• GWAS: LM, LMM, FastLMM, FarmCPU
• Genomic selection: GBLUP, adBLUP, rrBLUP, BayesA/B/Cpi, and ML models (RF/ET/GBDT/XGB/SVM/ENET)
• Streaming genotype IO for VCF/HMP/PLINK/TXT/NPY
• Post-analysis workflows: postgwas, postgarfield, postbsa
• Utility workflows: grm, pca, gformat, gmerge, hybrid, fastpop, webui, sim, simulation
• Launcher pipelines: fastq2vcf, fastq2count

---

Installation

Quick installation: Python with uv (Recommend)

• Linux | MacOS

curl -fsSL https://raw.githubusercontent.com/FJingxian/JanusX/main/scripts/install.sh | sh

• Windows

Set-ExecutionPolicy RemoteSigned -scope CurrentUser
irm https://raw.githubusercontent.com/FJingxian/JanusX/main/scripts/install.ps1 | iex

Option A: Python package install

pip install janusx==1.0.25

Option B: Conda / Bioconda

Recommended Bioconda channel order:

conda create -n janusx \
  --channel conda-forge \
  --channel bioconda \
  janusx

---

Quick start

1) GWAS

# Estimate variance for every snp, similar with GEMMA. (Exact, recommand)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -lmm -o test
# Estimate variance for every snp, similar with GEMMA. (Exact, wald and LR test, recommand)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -lmm2 -o test
# Estimate variance once in NULL model, similar with EMMAX. (Fast)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -fvlmm -o test
# Linear mixed model with sparse GRM, fastGWA-compatible sparse REML null + approximate GRAMMAR-gamma scan.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm-approx -o test
# Linear mixed model with sparse GRM, fastGWA-compatible sparse REML null + exact g'Pg scan.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm -o test
# FarmCPU (Fast, and more sites, prepared for biobank cohorts)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -farmcpu -o test

2) Post-GWAS

jx postgwas -i test/mouse_hs1940.test0.lmm.tsv -manh -qq -thr 1e-6 -o testpost

3) Genomic selection

# BLUP method, prepared for biobank cohorts
# n≤15,000 GBLUP
# n>15,000 & m≤15,000 rrBLUP
# n>15,000 & m>15,000 rrBLUP with PCG (Jacobi)
jx gs -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -BLUP -o test -cv 5
# Bayesian methods
jx gs -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -BayesA -BayesB -BayesCpi -o test -cv 5

* Genomic Selection for trait: test0
Train size: 1410, Test size: 530, EffSNPs: 8960
** BLUP
✔︎ Cross-validation ...Finished [0.8s]
✔︎ Fitting ...Finished [0.3s]
✔︎ Predicting ...Finished [0.0s]
** BayesA
✔︎ Cross-validation ...Finished [17.9s]
✔︎ Fitting ...Finished [4.1s]
✔︎ Predicting ...Finished [0.0s]
...
------------------------------------------------------------
Fold Method     Pearsonr Spearmanr R2     time(s)  Best
1    BLUP       0.704    0.675     0.493  0.198    
1    BayesA     0.709    0.680     0.493  3.507    
...
------------------------------------------------------------

4) Get module help

jx -h
jx <module> -h

See full usages in CLI Guide.

---

Module map

Genome-wide Association Studies (GWAS):

• grm
• pca
• gwas
• postgwas (Visualization, manh qq ldblock)
• fastpop (population-structure analysis; jx adamixture kept as compatibility alias)

Attribution note:

• FastPop is JanusX's own population-structure workflow and public name for this module.
• Historical JanusX releases referenced ADAMIXTURE as a related implementation; the BSD-3-Clause attribution notice is recorded in THIRD_PARTY_NOTICES.md.

Genomic Selection (GS):

• gs
• postgs (Visualization)
• reml (Estimation of broaden heritability and blup values)

GARFIELD:

• garfield (Based on https://github.com/heroalone/Garfield)
• postgarfield

Utility:

• gformat (Conversion between genotype data formats, support fast splicing/filtering/prune)
• gmerge (Merge genotype between samples)
• gstats (State freq/het/missing/ldscore of genotype)

---

Citation

@article {FuJanusX,
  title = {JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection},
  author = {Fu, Jingxian and Jia, Anqiang and Wang, Haiyang and Liu, Hai-Jun},
  year = {2026},
  doi = {10.64898/2026.01.20.700366},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2026/01/23/2026.01.20.700366},
  journal = {bioRxiv}
}

---

License

This project is licensed under GNU Affero General Public License v3.0 (AGPL-3.0-or-later). See LICENSE.