Shi Huang's repositories
2bRAD-M-manuscript
This repository provided all source data and codes for generation of all results in the 2bRAD-M manuscript.
2bRAD-M-paper
This repository provided all source data and codes for generation of all results in the 2bRAD-M manuscript. The preprint version of this paper has been available at biorxiv: Species-resolved sequencing of low-biomass microbiomes by 2bRAD-M by Zheng Sun, Shi Huang, Pengfei Zhu, Lam Tzehau, Helen Zhao, Jia Lv, Rongchao Zhang, Lisha Zhou, Qianya Niu, Xiuping Wang, Meng Zhang, Gongchao Jing, Zhenmin Bao, Jiquan Liu, Shi Wang, Jian Xu. BioRxiv, doi: https://doi.org/10.1101/2020.12.01.405647
2bRAD_denovo
Genome-wide de novo genotyping with 2bRAD
alphafold
Open source code for AlphaFold.
CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
curatedMetagenomicData
Curated and processed metagenomic data through ExperimentHub
ipyrad
Interactive assembly and analysis of RAD-seq data sets
kraken2
The second version of the Kraken taxonomic sequence classification system
mlrMBO
Toolbox for Bayesian Optimization and Model-Based Optimization in R
PM_Rscript
The Rscripts for microbiota analysis
q2-breakaway
QIIME2 plug-in for breakaway
qurro-mackerel-analysis
Simple re-analysis of mackerel and seawater marker gene sequencing samples in QIIME 2 + Songbird + Qurro
SHOGUN
SHallow shOtGUN profiler
stability-analyses
code for simulation studies and experimental microbiome data applications in Stability manuscript
TrimGalore
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data