/dolphinnext

A graphical user interface for distributed data processing of high throughput genomics

Primary LanguageJavaScriptGNU General Public License v3.0GPL-3.0

DolphinNext

A platform to create reproducible, portable and highly parallel pipelines

Build Status

DolphinNext, an intuitive web interface designed for users with limited bioinformatics experience to analyze and manage large numbers of samples on High Performance Computing (HPC) environments, cloud services or on a personal workstation.

  • A platform to manage processing pipelines for large projects that require a scalable solution with automatic monitoring of large number of concurrent jobs
  • A drag and drop user interface to create NextFlow pipelines.
  • Run pipelines with different executors such as SGE, LSF, SLURM, Ignite etc.

Benefits of the design:

  • Build: Easily create new pipelines using a drag and drop interface. No need to write commands from scratch, instead reuse existing processes/modules to create new pipelines

  • Run: Execute pipelines in any host environment. Seamless Amazon Cloud integration to create a cluster (EC2), execute the pipeline and transfer the results to the storage service (S3).

  • Resume: A continuous checkpoint mechanism keeps track of each step of the running pipeline. Partially completed pipelines can be resumed at any stage even after parameter changes.

  • Improve: Revisioning system keeps track of pipelines and processes versions as well as their parameters. Edit, improve shared pipelines and customize them according to your needs.

  • Share: Share pipelines across different platforms. Isolate pipeline-specific dependencies in a container and easily replicate the methods in other clusters

Public Pipelines:

  • RNA-Seq Pipelines (RSEM, HISAT, STAR, Tophat2)
  • ATAC-Seq Pipeline
  • ChIP Seq Pipeline
  • Single Cell Pipelines (10X Genomics, Indrop)
  • piRNA Pipelines (piPipes ChIP-Seq, Degradome/RAGE/CAGE, smallRNA)
  • Sub Modules:
    • Trimmer
    • Adapter Removal
    • Quality Filtering
    • Common RNA Filtering
    • ESAT
    • FastQC,
    • MultiQC
    • RSeQC
    • Picard
    • IGV and UCSC genome browser file conversion

Overview:

Overview Video

Highlights:

Workflow design with UI:

RSEM

Modular System (Nested Workflows):

RSEM

Quick Start and Documentation

Quick start guide, can be reached at https://dolphinnext.readthedocs.io/en/latest/dolphinNext/quick.html

Complete documentation is available at https://dolphinnext.readthedocs.io

Support

UMMS Biocore, provides support for installations as well as commercial support for DolphinNext. Please contact support@dolphinnext.com

Licensing

DolphinNext released under GNU General Public License 3.0.