Stars
Free and Open Source, Distributed, RESTful Search Engine
a fast, scalable, multi-language and extensible build system
Logstash - transport and process your logs, events, or other data
Generate diagrams from textual description
configuration library for JVM languages using HOCON files
Apache Groovy: A powerful multi-faceted programming language for the JVM platform
Zotero plugin to manage your attachments: automatically rename, move, and attach PDFs (or other files) to Zotero items, sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad,…
Official code repository for GATK versions 4 and up
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
A quality control analysis tool for high throughput sequencing data
Genome-scale protein function classification
RTG Tools: Utilities for accurate VCF comparison and manipulation
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
A Java API for high-throughput sequencing data (HTS) formats.
Various algorithms for analysing genomics data
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
Software for aligning viewing and editing dna/aminoacid sequences, intuitive, fast and lightweight. Download and website:
Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
An app store for scientific workflows, tools, notebooks, and services
MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities