Linux kernel source tree

Command line interface to GeneBe -- Genetic Variant Interpretation Tool

A Tool to Annotate and Prioritize Exome Variants

RFMIX - Local Ancestry and Admixture Inference Version 2

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

Segmented HAPlotype Estimation and Imputation Tool

The Pharmacogenomic Clinical Annotation Tool

A comprehensive tutorial about GWAS and PRS

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

Sanity check Variant Call Format (VCF) files.

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

A suite of tools for processing genotype data. Includes calling genotypes from .idat to plink (ped), sample/case-control variant QC steps, ancestry estimation. UNDER DEVELOPMENT

customizable pipeline to identify viral sequences from (meta)genomic data

A DSL for data-driven computational pipelines

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

SPAdes Genome Assembler

Ultra-fast and memory-efficient (meta-)genome assembler

Genome annotation with AUGUSTUS

Estimate recombination rates from population genetic data

PHAST

Haplotype based scans for selection

Rare variant test software for next generation sequencing data

deep residual neural network for classifying the pathogenicity of missense mutations.

Read-based phasing of genomic variants, also called haplotype assembly

phasing and Allele Specific Expression from RNA-seq

The hackable text editor

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…

Coding with all analyses performed in a project that aimed to study monkey proteins in a large number of genomes