Pinned Repositories
barclay
Command line argument parser and online documentation generation utilities for java command line programs.
gatk
Official code repository for GATK versions 4 and up
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.
AndroidSharedServices
Library for Android apps containing a simple re-useable single fragment activity.
BioScala
Scala library for bioinformatics, biological sequence analysis and transformation.
bramtools
Playground for genomics using Rust.
Catex.jl
cmnbroad
hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
cmnbroad's Repositories
cmnbroad/AndroidSharedServices
Library for Android apps containing a simple re-useable single fragment activity.
cmnbroad/BioScala
Scala library for bioinformatics, biological sequence analysis and transformation.
cmnbroad/bramtools
Playground for genomics using Rust.
cmnbroad/Catex.jl
cmnbroad/cmnbroad
cmnbroad/CppCoreGuidelines
The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++
cmnbroad/disq
A library for manipulating bioinformatics sequencing formats in Apache Spark
cmnbroad/GPTestTools
Tools and file utilities for use with GenePattern and GpUnit testing.
cmnbroad/Hadoop-BAM
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.
cmnbroad/hellbender
GATK4 development
cmnbroad/Docker
Docker files for various environments.
cmnbroad/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
cmnbroad/htscodecs
Custom compression for CRAM and others.
cmnbroad/htsjdk
A Java API for high-throughput sequencing data (HTS) formats.
cmnbroad/htsjdk-next-beta
Staging ground for the development of the next major version of HTSJDK
cmnbroad/jopt-simple
Java library for parsing command line options
cmnbroad/pgen-jni
Experimental jni wrapper of PGEN libraries
cmnbroad/pgen-runner
cmnbroad/RESTExplorer
Simple Android app for calling and returning data from a REST endpoint. Requests can be stored for future retrieval.
cmnbroad/SAMDescribe
Tools for analyzing metadata for SAM/BAM/CRAM alignment files.