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Computational Genome Analysis Platform

The Computational Genome Analysis Platform (CGAP) is an intuitive, open-source analysis tool designed to support complex research & clinical genomics workflows.

Computational Genome Analysis Platform

The Computational Genome Analysis Platform (CGAP) is an open-source platform developed primarily by Harvard's Department of Biomedical Informatics. CGAP consists of multiple repositories - the codebase of the portal itself, as well as repositories containing code which runs and defines the genomics pipelines, monitoring, and various utilities. Want to contribute to our open source community efforts? Contact us at cgap-support@hms-dbmi.atlassian.net.

Repositories

Pipelines & Analysis

  • cgap-pipeline-main - Main repository for bioinformatics pipelines and the relevant documentation.
  • cgap-pipeline-contribution - Pipeline modules contributed to CGAP through external collaboration.
  • granite - Software package to work with genomic variants. The package provides inheritance mode callers and utilities to filter and refine variants called by other methods in VCF format.
  • tibanna - Software package that runs pipelines on Amazon Web Services (AWS).
  • magma - Software package to manage meta-workflows automation and execution.

Portal Infrastructure

  • CGAP Portal - The primary codebase of the portal.
  • utils - A set of utility functions & scripts which are used in CGAP Portal and others.
  • snovault - Contains abstractions for communicating with our databases, including PostgreSQL and ElasticSearch. A major dependency of CGAP Portal. Originally this was forked from ENCODE Project in ~2015.
  • react-workflow-viz - A React component/library for visualizing workflow runs.

Visualization

Applications

  • SubmitCGAP - Command-line tools for submitting and uploading files to CGAP.

Administrative

  • Governance - Repository of governance, legal and policy information for our projects.
  • Legal Notices - Legal notices for portal users.

Pinned Loading

  1. cgap-portal cgap-portal Public

    Data portal for the DBMI-BGM CGAP initiative

    Python 7

  2. cgap-pipeline-main cgap-pipeline-main Public

    main repository for cgap pipeline

    Makefile

  3. cgap-pipeline-contribution cgap-pipeline-contribution Public

    pipeline modules contributed to cgap through external collaboration

    Shell 1

Repositories

Showing 10 of 43 repositories
  • cgap-portal Public

    Data portal for the DBMI-BGM CGAP initiative

    dbmi-bgm/cgap-portal’s past year of commit activity
    Python 7 MIT 0 0 49 Updated Nov 11, 2024
  • foursight-cgap Public

    Providing insight into your application using AWS infrastructure.

    dbmi-bgm/foursight-cgap’s past year of commit activity
    Python 2 MIT 0 0 7 Updated Oct 14, 2024
  • granite Public Forked from bgm-cwg/novoCaller

    A collection of software to work with genomic variants

    dbmi-bgm/granite’s past year of commit activity
    Python 6 MIT 1 0 1 Updated Sep 11, 2024
  • magma Public

    A collection of tools to manage meta-workflows automation

    dbmi-bgm/magma’s past year of commit activity
    Python 0 MIT 1 0 1 Updated Aug 15, 2024
  • dbmi-bgm/udn-browser’s past year of commit activity
    JavaScript 0 MIT 0 0 0 Updated Aug 13, 2024
  • SubmitCGAP Public

    Support for file submissions related to CGAP.

    dbmi-bgm/SubmitCGAP’s past year of commit activity
    Python 0 MIT 1 0 2 Updated Jul 3, 2024
  • cgap-pipeline-upstream-sentieon Public

    upstream pipeline using Sentieon

    dbmi-bgm/cgap-pipeline-upstream-sentieon’s past year of commit activity
    Shell 0 MIT 0 0 0 Updated Mar 21, 2024
  • cgap-pipeline-base Public

    base pipeline components

    dbmi-bgm/cgap-pipeline-base’s past year of commit activity
    Python 0 GPL-3.0 1 0 1 Updated Feb 15, 2024
  • portal-pipeline-utils Public

    pipeline utilities

    dbmi-bgm/portal-pipeline-utils’s past year of commit activity
    Python 0 MIT 1 0 0 Updated Feb 14, 2024
  • cgap-pipeline-main Public

    main repository for cgap pipeline

    dbmi-bgm/cgap-pipeline-main’s past year of commit activity
    Makefile 0 GPL-3.0 0 1 0 Updated Dec 4, 2023

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