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

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# DolphinNext

### A platform to create reproducible, portable and highly parallel pipelines

**Citation:** Yukselen, O., Turkyilmaz, O., Ozturk, A.R. et al. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x

[![Build Status](https://api.travis-ci.com/UMMS-Biocore/dolphinnext.svg?branch=master)](https://api.travis-ci.com/UMMS-Biocore/dolphinnext)[![DOI:10.1186/s12864-020-6714-x](https://zenodo.org/badge/DOI/10.1186/s12864-020-6714-x.svg)](https://doi.org/10.1186/s12864-020-6714-x)

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[DolphinNext](https://dolphinnext.umassmed.edu/), 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 and Google Cloud integration to create a cluster (instance), execute the pipeline and transfer the results to the storage services (S3 or GS).

* **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](https://raw.githubusercontent.com/UMMS-Biocore/dolphinnext/master/docs/dolphinNext/dolphinnext_images/youtube-overview.png)](https://www.youtube.com/watch?v=1ak1m5pvkw4&t)

## Highlights:

##### Workflow design with UI:

# ![RSEM](https://raw.githubusercontent.com/UMMS-Biocore/dolphinnext/master/docs/dolphinNext/dolphinnext_images/pipeline_rsem.png)

##### Modular System (Nested Workflows):

# ![RSEM](https://raw.githubusercontent.com/UMMS-Biocore/dolphinnext/master/docs/dolphinNext/dolphinnext_images/pipeline_rsem_nested.png)

## 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

[*Developer Tutorial*](https://github.com/UMMS-Biocore/dolphinnext-tutorial) is available which explains the basics of DolphinNext. You can use our [website](https://dolphinnext.umassmed.edu/), or easily pull Docker image of Dolphinnext and start creating pipelines in your local server.

## Citation:

If you use DolphinNext in your research, please cite:

Yukselen, O., Turkyilmaz, O., Ozturk, A.R. et al. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x

## 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.

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