jaredo's Stars
odelaneau/shapeit5
Segmented HAPlotype Estimation and Imputation Tool
Illumina/hap.py
Haplotype VCF comparison tools
tskit-dev/tskit
Population-scale genomics
bwa-mem2/bwa-mem2
The next version of bwa-mem
Rdatatable/data.table
R's data.table package extends data.frame:
odelaneau/shapeit4
Segmented HAPlotype Estimation and Imputation Tool
Genomicsplc/wecall
Fast, accurate and simple to use command line tool for variant detection in NGS data.
base2genomics/batchit
simple jobs submission via command-line for AWS batch
mcveanlab/TreeWAS
mkj/dropbear
Dropbear SSH
statgen/bravo
Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Online
Illumina/gvcfgenotyper
A utility for merging and genotyping Illumina-style GVCFs.
imbs-hl/ranger
A Fast Implementation of Random Forests
isocpp/CppCoreGuidelines
The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++
luntergroup/octopus
Bayesian haplotype-based mutation calling
qtltools/qtltools
A complete tool set for molecular QTL discovery and analysis
broadinstitute/gatk-protected
Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
poruloh/Eagle
Haplotype phasing software
chrchang/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. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.
Illumina/akt
Ancestry and Kinship Tools
lh3/bgt
Flexible genotype query among 30,000+ samples whole-genome
hall-lab/speedseq
A flexible framework for rapid genome analysis and interpretation
Illumina/agg
gvcf aggregation tool
marbl/canu
A single molecule sequence assembler for genomes large and small.
jeromekelleher/msprime-paper
Comparisons of simulators for the msprime paper
lh3/minimap
This repo is DEPRECATED. Please use minimap2, the successor of minimap.
freebayes/freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
ekg/1000G-integration
variant integration methods for the 1000 Genomes Project
pmelsted/KmerStream
Streaming algorithm for computing kmer statistics for massive genomics datasets
Illumina/isaac2
Aligner for sequencing data