lib for scripting vcf access from rust and node module for vcf access from js/ts

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

A JBrowse 2 graph genome viewer (WIP)

Format SQL using the rust sqlformat library

A genomic k-mer counter (and sequence utility) with nice features.

k-mer based assembly evaluation

A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

Repeat-aware polishing genomes assembled using HiFi long reads

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…

PCAtools: everything Principal Components Analysis

Publication-ready volcano plots with enhanced colouring and labeling

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Algorithm For Gene Order Reconstruction in Ancestors

Technology agnostic long read analysis pipeline for transcriptomes

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium

An R package for downstream data analysis of microbiome omics data

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

Population-scale genotyping using pangenome graphs

A list of software for pangenomics

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Test sets and pipeline scripts for pan-genomic graph analysis

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

Detecting sites of genomic enrichment

Variant calling tool for long-read sequencing data