HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

SNPbinner is a utility for the generation of genotype crossover points and binmaps based on SNP data across recombinant inbred lines.

PriOritizing the Candidate genes by incorporating information of Knowledge-based gene sets, Effects of variants, GWAS and TWAS

A library for running k-mers based GWAS

Foldseek enables fast and sensitive comparisons of large structure sets.

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

displays multiple genomic sequences in the form of a tube map

A fast GWAS software for binary traits in case-control dataset

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

An Example of Subgenome Phasing for Complex Allopolyploidy

This pipeline is used to distinguish allotetraploid subgenomes.

RNA-seq aligner

An ultra-fast and efficient genomic tool for coverage calculation

R package for binmap

a programme for visualization of short sequence alignment and path navigation in graphical pan-genome

Use hifi to assembly the Sol genome, and dissecting Sol evo

tools for working with genome variation graphs

One-step to Cluster and Visualize Gene Expression Matrix