zhenpeng yu's repositories
dadi_pipeline
An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.
TAD-and-loop-identification-workflows
TAD-loop identification
A-genome-assebmly-and-annotation-pipeline
A pipeline for assembling and annotating vertebrate genomes using Illumina short reads, PacBio or Nanopore long reads and HiC data
Angiosperm-karyotype-evolution
核型进化Angiosperm karyotype evolution
bioinfo_tools
TEs analysis
Canada_SARS-Cov-2
规范分析与代码写作模板
chromsyn
Chromosome-level synteny plotting using orthologous regions可视化
DeepTE
Neural network classification of TE
DGINN
获取直系同源基因序列、多序列比对
dysgu
dysgu-SV is a collection of tools for calling structural variants using short or long reads
FalseGeneLoss
Data and scripts for an unpublished paper about false chromosome and gene losses in assemblies caused by sequence and assembly errors
FastANI
Fast Whole-Genome Similarity (ANI) Estimation
Finder
整合多个转录组基因结构注释
Gene-Synteny-Analysis
MCscan 可视化
gtftools
GTF tools
HCGS-Comparative-Genomics
NCBI download and Orthofinder analysis
HiCassembly
Pipeline using HiC data to help the genome assembly
kallisto
Near-optimal RNA-Seq quantification
killer_tools
Killer tools/packages/libraries/websits/...
LiftoffTools
LiftoffTools
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
PsiCLASS
多个转录组样本组装
public_scripts
collection of bioinformatic scripts
steppingStone
A pipeline to identify chromothripsis breakpoints and trace cancer rearrangements
T2T-Polish
Evaluation and polishing workflows for T2T genome assemblies
turtle-genomics
Web resources for the comparative turtle genomics project
two-species-genome-comparison-pipeline
Two-species genome comparison pipeline (combines minimap2/SyRI, EDTA, bedtools) to identify structural variants (inv/syn), annotate TE, and plot results in R.