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yunzhengluoyi's Projects

adam icon adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

bcftools icon 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

bio icon bio

Bioinformatics library for .NET

bwa icon bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

gamgee icon gamgee

A C++14 library for NGS data formats

gatk icon gatk

GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses

gatk-protected icon gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

java icon java

Development repository for Opscode Cookbook java

mutect icon mutect

MuTect -- Accurate and sensitive cancer mutation detection

mutest icon mutest

A prototype database for storing somatic variants.

pairhmm icon pairhmm

Optimization of a Haplotype PairHMM class for GPU processing

picard icon picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

piper icon piper

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper

rtg-tools icon rtg-tools

RTG Tools: Utilities for accurate VCF comparison and manipulation

samtools icon samtools

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

variationanalysis icon variationanalysis

This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate deep learning models trained with semi-simulation. See docs below for details.

vcftools icon vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

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