IDR

Intro to ChIPseq using HPC

Ultraperformant reimplementation of SICER

A DSL for data-driven computational pipelines

ChIP-seq peak-calling, QC and differential analysis pipeline.

CrossMap is a python program to lift over genome coordinates from one genome version to another.

DNA序列比对结果 可视化展示工具

An Integrative Toolkit for Assembling Plant Mitochondrial Genomes Using HiFi Reads

Using Deep Learning to predict gene annotations

Program for analysing NGS data.

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Methods and recipes for Plant Genome Annotation - Transposable Elements

TEtrimmer: a novel tool to automate manual curation of transposable elements

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

Repeat-aware polishing genomes assembled using HiFi long reads

NLR-Annotator upload

An R package to visualize chromosome scale repeat patterns and predict centromere locations.

Tool for decomposition centromeric assemblies and long reads into monomers

ULTRA Locates Tandemly Repetitive Areas

Extensive de-novo TE Annotator

Scripts for the Linkage drag paper https://doi.org/10.1073/pnas.2205783119

Convert Tandem Repeat Finder dat file output into gff3 format

RepeatIdentifier

SRY: an effective method for sorting long-read of sex-limited (Y or W) chromosome. (Developed by WANG Xiaobo from CAAS)

MutMap pipeline to identify causative mutations responsible for a phenotype

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files