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akt

Ancestry and Kinship Tools

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bcftools-plugins

some random bcftools plugins

bravo

BRowse All Variants Online

docker-alignment

Dockerfile for Alignment

duohmm

A post-hoc pedigree phasing routine for use with SHAPEIT2

eagle

Haplotype phasing software

gatk4-genotypegvcfs-nf

Joint calling of gVCF, following GATK4 Best Practices

googletest

Google Test

gvcfgenotyper

A utility for merging and genotyping Illumina-style GVCFs.

gwas

Some useful code for GWAS

hap.py

Haplotype VCF comparison tools

jaredo.github.io

Personal web page

jeigen

Java wrapper for Eigen C++ fast matrix library

nxtrim

Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.

pipeline-standardization

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase).

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

shapeit4

Segmented HAPlotype Estimation and Imputation Tool

snptools

Automatically exported from code.google.com/p/snptools

test

test repository

thesis

DPhil thesis