bedtools - the swiss army knife for genome arithmetic

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

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

genotype and visualize structural variants in the human pangenome graphs

A context-based long-read simulator

A rapid and low-memory multiple-genome aligner for closely related genomes

Fast Tandem Repeat Finder

Build satellite library

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

gghic makes visualization of Hi-C/-like data easily in R

Genomic Association Tester

Scripts for manually classifying reads and make figures

A multiscale pangenome browser

Genome annotation pre-publication results

Share your terminal over the web

Foreign Contamination Screening caller scripts and documentation

Estimating telomere content from genome sequencing data

High throughput python tool for mining and analysis of gene duplications.

Multi-level visualization of genomic statistical variables on rectangular chromosomes

Fast and haplotype-aware assembler

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

A tool for sniffing out the differences in vari-Ants

Find endogenous viral elements in genomes

Tandem Repeats Finder: a program to analyze DNA sequences

A package for the extension of repetitive DNA sequences

A "dot"-plot style viewer for .1aln files