A lightweight wrapper to run minimap2 (v2.30) alignments directly on BAM file

PYQA — Local development / test driver script

A KMER-based genome-wIde Assocation testing approach on polyploids

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

RUNE (Retrieve UNique k-mErs) is a simple tool for extracting unique k-mers in one fasta file.

AlleleFinder is a tool for identifying allele genes from polyploid genome.

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).

Classify chimeric reads based on unique kmer contents

Neural network classification of TE

Python library to facilitate genome assembly, annotation, and comparative genomics

MATE (Meaningful Allelic-haploType dEtector) is a tool for identifying allelic haplotype associate with phenotypes.

several scripts for bioinformatics

Yet another Hi-C scaffolding tool

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

A plot package for bioinformatics

popCNV is a tool for calculating copy number of genes and get genes selected by humans

T2Tools is a toolset contains several tools for T2T assembly, and it is under development.

CATG (Collinearity-based Assembly correcTor GUI) is a tool that can correct genome assembly with collinearity and generate tour files for assembly.

Automatic DNA methylation detection from nanopore tools and their consensus model

BAM Statistics, Feature Counting and Annotation

A Rich renderable for viewing Multiple Sequence Alignments in the terminal.

A fast and efficient tool for converting chromatin interaction data between genome assemblies

Automated Pipeline for Variant/Haplotype Calling and Filtering

FAN-C: Framework for the ANalysis of C-like data

Fast and accurate gene fusion detection from RNA-Seq data

A program to call variants from genome alignment