Pinned Repositories
AdmixSim2
forward-time simulator of population genetic data
ArchaicSeeker2.0
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 introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.
Chinese-Pangenome-Consortium-Phase-I
CPC-graph-based-NGS-pipeline
A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
MultiWaver2.0
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 discrete models and continuous models.
NGS.PRSS1-2caller
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.
PanGenome_VCF_PostProcess
A simple pipeline to process the VCF deconstructed from the VG pangenome graph
PGGSVpipeline
Theta_D_H.Est
Calculator for statictics including Theta, D, H, and so on, based on the VCF input.
Y-LineageTracker
A high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Shuhua-Group's Repositories
Shuhua-Group/Chinese-Pangenome-Consortium-Phase-I
Shuhua-Group/ArchaicSeeker2.0
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 introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.
Shuhua-Group/CPC-graph-based-NGS-pipeline
A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
Shuhua-Group/PGGSVpipeline
Shuhua-Group/Theta_D_H.Est
Calculator for statictics including Theta, D, H, and so on, based on the VCF input.
Shuhua-Group/AdmixSim2
forward-time simulator of population genetic data
Shuhua-Group/PanGenome_VCF_PostProcess
A simple pipeline to process the VCF deconstructed from the VG pangenome graph
Shuhua-Group/Construct-ancestral-genome
Construct the ancestral genome from the given populations.
Shuhua-Group/SVanalysis_STARProtocols
A protocol for applying low-coverage whole-genome sequencing data in structure variation studies
Shuhua-Group/AdmixInfer
Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
Shuhua-Group/HierarchyMix
reconstruct the 4-way complex admixture history
Shuhua-Group/MultiWaver2.0
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 discrete models and continuous models.
Shuhua-Group/TMRCA
time to the most recent common ancestor
Shuhua-Group/AncestryPainterV2
An updated version of AncestryPainterV1, a graphing tool to display ancestry composition and genetic difference.
Shuhua-Group/CHIP-mutation-calling-NGS-pipeline
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.
Shuhua-Group/MultiWaver
Inference of multiple-wave admixtures by length distribution of ancestral tracks
Shuhua-Group/MultiWaverX
Inference on the sex-biased admixture history
Shuhua-Group/NGS.PRSS1-2caller
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.
Shuhua-Group/PGG.MHC
Shuhua-Group/RNA-Seq
Shuhua-Group/SC-sample
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:http://www.biomedcentral.com/1471-2105/15/273
Shuhua-Group/SC-Spatial_Coalescent_simulator
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 and MaCS misses some information) such as the distribution of ARG generated by SC is identical to that generated by a typical back-in-time model adopted by ms. SC is developed based on Macs-0.4e, all macs options are not changed. Thanks to Gary Chen to provide support.
Shuhua-Group/TJ1
Shuhua-Group/HERV-identification-and-calling-pipeline
Shuhua-Group/iMAAPs
To infer multiple-wave admixture by fitting ALD using a p-spectrum
Shuhua-Group/SimAncestry1.0
SimAncestry is a script to extract archaic introgressed sequences from ms simulation output.
Shuhua-Group/TJ1_STARProtocols
Shuhua-Group/Calculate.genetic.distance
This script can calculate the genetic distances of given variants based on their physical positions and genetic map files.
Shuhua-Group/Genetic-characteristics-of-the-Han100K-initiative
We calculated pairwise FST and Ancestry components for each provincial population.
Shuhua-Group/iMAAPssmry0.2
Version 0.2 of R package iMAAPssmry