JanusX

CLI Guide | Core API Guide | v2.0.0 Release

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:

• Genome-Wide Association Study (GWAS): lm, lmm, lmm2, fvlmm, SparseLMM (splmm / splmm-exact), farmcpu, and cis/trans pair scans (ct)
• Genomic Selection (GS): BLUP, BayesA/B/C/R, PLS/KRR, and ML models (RF/ET/GBDT/XGB/SVM/ENET)
• Streaming genotype IO for VCF/HMP/PLINK BED and PLINK 2 PGEN
• Post-analysis workflows: postgwas, postgs
• Utility workflows: grm, pca, gformat, gmerge, fastpop (including FST and XP-CLR)

Installation

Quick installation: Python with uv (recommend)

• Linux | MacOS

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

• Windows

powershell -ExecutionPolicy ByPass -c "irm https://raw.githubusercontent.com/FJingxian/JanusX/main/scripts/install.ps1 | iex"

Option A: Python package install

pip install janusx==2.0.0

Option B: Conda / Bioconda

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

Quick start

1) GWAS

# Estimate variance for every SNP.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -lmm -o test/
# Exact LMM with Wald and likelihood-ratio results.
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, recommend)
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -fvlmm -o test/
# SparseLMM with sparse REML null and approximate GRAMMAR-gamma scan.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm -o test/
# SparseLMM with the exact sparse-Cholesky g'Pg scan denominator.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -splmm-exact -o test/
# FarmCPU.
jx gwas -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -farmcpu -o test/

For PLINK 2 PGEN input, use -pfile <prefix>; -bfile <prefix> reads PLINK BED files.

2) Post-GWAS

jx postgwas -i test/mouse_hs1940.test0.lmm.tsv -manh -qq -thr 1e-6 -o testpost/
jx postgwas -i test/mouse_hs1940.test0.lmm.tsv test/mouse_hs1940.test1.lmm.tsv -manh-merge -qq-merge -fontsize 11 -fontstyle arial -o testpost/
jx postgwas -i test/mouse_hs1940.test0.lmm.tsv test/mouse_hs1940.test1.lmm.tsv test/mouse_hs1940.test2.lmm.tsv -manh-merge -qq-merge -scatter-size 4 10 -alpha 0.2 0.5 -ylim 2 10 -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 (BayesR in JanusX-2.0.0 uses pi=(0.95,0.03,0.01,0.01), gamma=(0,0.01,0.1,1))
jx gs -vcf example/mouse_hs1940.vcf.gz -p example/mouse_hs1940.pheno -BayesA -BayesB -BayesC -BayesR -o test/ -cv 5
# BayesB fixes pi at 0.05 by default; append a value to override it. BayesC
# estimates pi unless a value is supplied:
# jx gs ... -BayesB 0.05 -BayesC 0.10

* 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
• ct (cis/trans pair scans)
• postgwas (Visualization, manh qq ldblock)
• fastpop (population structure, FST, and XP-CLR)

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)

Epistasis:

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

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,
author = {Fu, Jingxian and Jia, Anqiang and Wang, Haiyang and Liu, Hai-Jun},
title = {JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection},
journal = {The Plant Journal},
volume = {127},
number = {5},
pages = {e71105},
doi = {https://doi.org/10.1111/tpj.71105},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.71105},
year = {2026}
}

License

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