A newly designed version of Bamsnap with Long Read Support (LRS) which inspired by bamsnap (https://github.com/parklab/bamsnap)

NEAT (NExt-generation Analysis Toolkit) simulates next-gen sequencing reads and can learn simulation parameters from real data.

A realistic-ish aDNA simulator

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

A structural variant filtering and prioritization tool for long-read sequencing data

Tool for plotting sequencing data along genomic coordinates.

Multi-level visualization of genomic statistical variables on rectangular chromosomes

genotype and visualize structural variants in the human pangenome graphs

浙江大学人工智能算法与系统大作业（2025年秋）

Reference-free profiling of polyploid genomes

Open Human Genome Library

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Genome assembly and variant benchmarks for Chinese Quartet

Dimension reduction (by LLM)

Coalescent Likelihood Under Effects of Selection - Inferring selection & allele frequency trajectories from nucleotide data

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

A tool for pangenome graph-based phased diploid genome inference.

Copy Number Tool

Structural Variation Modeller (SVModeller)

Fast inference of fine-scale recombination rates based on fused-LASSO

Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.

Simulate genealogical trees and genomic sequence data using population genetic models

Convert HAL to VG

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Assemblies from HPP Year 1 production

Pile of codes

Genome browser hub for the T2T genomes and resources

Transfer HiFi read mappings from their own assembly contigs to a standard reference