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    47 repositories

    • NRS-identification-pipeline

      Public
      The NRS (Non-Reference Sequence) identification pipeline is a two-stage analysis pipeline for identifying and analyzing non-reference sequences in the human gen…
      C++
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • ArchaicSeeker3.0

      Public
      A Mamba-Based Algorithm for Archaic Introgression Detection
      Python
      •
      Other
      •1•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • HiMWA

      Public
      C++
      •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • AdmixSim2

      Public
      forward-time simulator of population genetic data
      C++
      •
      GNU General Public License v3.0
      •3•7•5•0•Updated Dec 19, 2025Dec 19, 2025

    • AncestryPainterV2

      Public
      An updated version of AncestryPainterV1, a graphing tool to display ancestry composition and genetic difference.
      R
      •
      GNU General Public License v3.0
      •2•4•1•0•Updated Nov 4, 2025Nov 4, 2025

    • CPC-graph-based-NGS-pipeline

      Public
      A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
      Python
      •4•17•1•0•Updated Aug 30, 2025Aug 30, 2025

    • PGGAF1M-allele-frequency-pipeline

      Public
      Shell
      •0•0•0•0•Updated Aug 8, 2025Aug 8, 2025

    • ArchaicSeeker2.0

      Public
      ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series,…
      C++
      •
      GNU General Public License v3.0
      •3•20•2•0•Updated Aug 6, 2025Aug 6, 2025

    • PGG.Selection.Burden

      Public
      Python
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • PGG.Panel

      Public
      Shell
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • CHIP-mutation-calling-NGS-pipeline

      Public
      This pipeline based on snakemake calls CHIP variants from next-generation whole-exome/genome sequencing of human samples and produces a purely filtered VCF file…
      Shell
      •
      GNU General Public License v3.0
      •1•2•1•0•Updated Apr 11, 2025Apr 11, 2025

    • PanGenome_VCF_PostProcess

      Public
      A simple pipeline to process the VCF deconstructed from the VG pangenome graph
      Python
      •1•7•0•0•Updated Jan 20, 2025Jan 20, 2025

    • Construct-ancestral-genome

      Public
      Construct the ancestral genome from the given populations.
      Python
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Jan 18, 2025Jan 18, 2025

    • Calculate.genetic.distance

      Public
      This script can calculate the genetic distances of given variants based on their physical positions and genetic map files.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 18, 2025Jan 18, 2025

    • Chinese-Pangenome-Consortium-Phase-I

      Public
      Shell
      •11•73•1•0•Updated Sep 24, 2024Sep 24, 2024

    • HierarchyMix

      Public
      reconstruct the 4-way complex admixture history
      Python
      •0•2•0•0•Updated Jul 15, 2024Jul 15, 2024

    • HERV-identification-and-calling-pipeline

      Public
      Python
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • Genetic-characteristics-of-the-Han100K-initiative

      Public
      We calculated pairwise FST and Ancestry components for each provincial population.
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • SVanalysis_STARProtocols

      Public
      A protocol for applying low-coverage whole-genome sequencing data in structure variation studies
      population-geneticstranscriptomicsstructure-variation
      population-geneticstranscriptomicsstructure-variation
      Shell
      •1•3•0•0•Updated Feb 28, 2024Feb 28, 2024

    • MultiWaverX

      Public
      Inference on the sex-biased admixture history
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 14, 2023Feb 14, 2023

    • RNA-Seq

      Public
      Python
      •0•2•0•0•Updated Nov 11, 2022Nov 11, 2022

    • NGS.PRSS1-2caller

      Public
      NGS.PRSS1-2caller is a toolkit for calling genetic variants at PRSS1-PRSS2 locus, which enables detecting SNV, INDEL and CNV with high accuracy and sensitivity.
      Python
      •2•3•0•0•Updated Sep 23, 2022Sep 23, 2022

    • PGGSVpipeline

      Public
      Python
      •2•11•0•0•Updated Sep 23, 2022Sep 23, 2022

    • PGG.MHC

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Sep 18, 2022Sep 18, 2022

    • TMRCA

      Public
      time to the most recent common ancestor
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Jul 15, 2022Jul 15, 2022

    • Theta_D_H.Est

      Public
      Calculator for statictics including Theta, D, H, and so on, based on the VCF input.
      Python
      •
      GNU General Public License v3.0
      •2•7•1•0•Updated Jul 1, 2022Jul 1, 2022

    • TJ1_STARProtocols

      Public
      Python
      •3•0•0•0•Updated May 12, 2022May 12, 2022

    • MultiWaver2.0

      Public
      MultiWaver series software was designed to infer population admixture history in case of various and complex scenarios. The earlier version of MultiWaver consid…
      C++
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated May 6, 2022May 6, 2022

    • TJ1

      Public
      Python
      •0•1•0•0•Updated Mar 10, 2022Mar 10, 2022

    • iMAAPssmry0.2

      Public
      Version 0.2 of R package iMAAPssmry
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 22, 2021Nov 22, 2021
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