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    41 repositories

    • Construct-ancestral-genome

      Public
      Construct the ancestral genome from the given populations.
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Nov 28, 2024Nov 28, 2024

    • AncestryPainterV2

      Public
      An updated version of AncestryPainterV1, a graphing tool to display ancestry composition and genetic difference.
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • Chinese-Pangenome-Consortium-Phase-I

      Public
      Shell
      •10•63•0•0•Updated Sep 24, 2024Sep 24, 2024

    • CPC-graph-based-NGS-pipeline

      Public
      A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
      Python
      •2•15•1•0•Updated Sep 22, 2024Sep 22, 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

    • 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 containing high confident CHIP mutations.
      1•1•1•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

    • 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
      •1•0•0•0•Updated Mar 3, 2024Mar 3, 2024

    • SVanalysis_STARProtocols

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

    • PanGenome_VCF_PostProcess

      Public
      A simple pipeline to process the VCF deconstructed from the VG pangenome graph
      Python
      •1•5•0•0•Updated Nov 9, 2023Nov 9, 2023

    • ArchaicSeeker2.0

      Public
      ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgress…
      C++
      •
      GNU General Public License v3.0
      •3•17•0•0•Updated Oct 20, 2023Oct 20, 2023

    • AdmixSim2

      Public
      forward-time simulator of population genetic data
      C++
      •
      GNU General Public License v3.0
      •3•6•2•0•Updated Apr 3, 2023Apr 3, 2023

    • 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•1•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•1•0•0•Updated Sep 23, 2022Sep 23, 2022

    • PGGSVpipeline

      Public
      Python
      •2•10•0•0•Updated Sep 23, 2022Sep 23, 2022

    • PGG.MHC

      Public
      Python
      •
      MIT License
      •1•1•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 considered only the discrete admixture models. In the newly developed version MultiWaver 2.0, we implemented a more flexible framework to automatically select an optimal admixture model among d…
      C++
      •
      GNU General Public License v3.0
      •0•2•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

    • iMAAPs

      Public
      To infer multiple-wave admixture by fitting ALD using a p-spectrum
      Roff
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Nov 19, 2021Nov 19, 2021

    • SimAncestry1.0

      Public
      SimAncestry is a script to extract archaic introgressed sequences from ms simulation output.
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 11, 2021Nov 11, 2021

    • SC-Spatial_Coalescent_simulator

      Public
      SC (Spatial Coalescent simulator) is a computer simulation tool for modeling spatial coalescent with recombination process. The algorithm implemented in SC is an improvement of the Wiuf and Hein algorithm (Wiuf and Hein, 1999). SC is proven to be the only precise ancestral recombination graph (ARG) simulator (Wiuf and Hein’s has some redundant a…
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Nov 11, 2021Nov 11, 2021

    • SC-sample

      Public
      SC-sample is a computer simulation tool for modeling spatial coalescent with recombination process, which generates ARGs directly consistent with the given sample. It attempts to uniformly select ARG from the sample-consistent ARG space. The algorithm is modified version of SC. -----------Related Publication: BMC Bioinformatics. 15:273. Link:htt…
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Nov 11, 2021Nov 11, 2021

    • MultiWaver

      Public
      Inference of multiple-wave admixtures by length distribution of ancestral tracks
      C++
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Nov 11, 2021Nov 11, 2021

    • AdmixInfer

      Public
      Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
      C++
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Nov 11, 2021Nov 11, 2021