A comprehensive telomere annotation tool for genome assemblies and graphs.

A conda-forge distribution.

Hi-C data processing pipeline

Software GMATA for SSR mining, marker designing, genotyping, plot etc.

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

3D de novo assembly (3D DNA) pipeline

Visualization and analysis software for Hi-C data -

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Fast genome-wide functional annotation through orthology assignment

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

GenomeTools genome analysis system.

Make colorful identity heatmaps of genomic sequence

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, m…

Get assembly statistics from FASTA and FASTQ files

Tandem Repeats Finder: a program to analyze DNA sequences

Ploidy agnostic phasing pipeline and algorithm

Using Deep Learning to predict gene annotations

a fork of the gap-closing pipeline PBJelly

YAGCloser: Yet-Another-Gap-Closer based on spanning of long reads.

VGP repository for the genome assembly working group

Statistics and analysis for variation graphs

PhyloSD: Phylogenomic Subgenome Detection pipeline

python module to plot beautiful and highly customizable genome browser tracks

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

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

Evaluating genome assemblies