jaredo

jaredo's Stars

• odelaneau/shapeit5

  Segmented HAPlotype Estimation and Imputation Tool

  Language:C++619

• Illumina/hap.py

  Haplotype VCF comparison tools

  Language:C++402122

• tskit-dev/tskit

  Population-scale genomics

  Language:Python15170

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++71097

• Rdatatable/data.table

  R's data.table package extends data.frame:

  Language:R3.6k970

• odelaneau/shapeit4

  Segmented HAPlotype Estimation and Imputation Tool

  Language:C++8818

• Genomicsplc/wecall

  Fast, accurate and simple to use command line tool for variant detection in NGS data.

  Language:C++104

• base2genomics/batchit

  simple jobs submission via command-line for AWS batch

  Language:Go8010

• mcveanlab/TreeWAS

  Language:R156

• mkj/dropbear

  Dropbear SSH

  Language:C1.7k398

• statgen/bravo

  Deprecated. See new version: https://github.com/statgen/bravo_api - BRowse All Variants Online

  Language:HTML99

• Illumina/gvcfgenotyper

  A utility for merging and genotyping Illumina-style GVCFs.

  Language:C++312

• imbs-hl/ranger

  A Fast Implementation of Random Forests

  Language:C++768193

• isocpp/CppCoreGuidelines

  The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

  Language:CSS42.3k5.4k

• luntergroup/octopus

  Bayesian haplotype-based mutation calling

  Language:C++30239

• qtltools/qtltools

  A complete tool set for molecular QTL discovery and analysis

  Language:C++5022

• broadinstitute/gatk-protected

  Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

  Language:Java3320

• poruloh/Eagle

  Haplotype phasing software

  Language:C++6315

• 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.

  Language:C404122

• Illumina/akt

  Ancestry and Kinship Tools

  Language:C++6913

• lh3/bgt

  Flexible genotype query among 30,000+ samples whole-genome

  Language:C9610

• hall-lab/speedseq

  A flexible framework for rapid genome analysis and interpretation

  Language:C311116

• Illumina/agg

  gvcf aggregation tool

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• marbl/canu

  A single molecule sequence assembler for genomes large and small.

  Language:C++652178

• jeromekelleher/msprime-paper

  Comparisons of simulators for the msprime paper

  Language:TeX53

• lh3/minimap

  This repo is DEPRECATED. Please use minimap2, the successor of minimap.

  Language:C10629

• freebayes/freebayes

  Bayesian haplotype-based genetic polymorphism discovery and genotyping.

  Language:C++764261

• ekg/1000G-integration

  variant integration methods for the 1000 Genomes Project

  Language:Shell213

• pmelsted/KmerStream

  Streaming algorithm for computing kmer statistics for massive genomics datasets

  Language:C++5211

• Illumina/isaac2

  Aligner for sequencing data

  Language:C++214