Visualizing genomic datasets using the Seven Bridges Genomics Genome Browser
1. Introduction
The Seven Bridges Genomics Platform is a cloud platform for analyzing genetic data generated through next-generation sequencing technologies. Seven Bridges provides a one-stop solution for managing NGS projects by enabling users to create and run complex data analysis pipelines easily using a drag-and-drop interface.1
This guide demonstrates how to use the Seven Bridges Genomics Platform to run a pipeline that processes an input BAM file to produce a sorted BAM and a respective BAM.BAI file for visualizing using the Genome Browser.
The guide uses the popular Coriell Cell Repository NA12878 reference sample, which has been extensively analyzed by the Genome in a Bottle Consortium.
2. Creating projects
A user must register an account or log in to use the Seven Bridges Platform. Once an account is set up, a new project can be created by clicking on Create Project from the Projects menu. A new Name and the Billing Group must be specified before creating a new project.
3. Creating pipelines
Pipelines are executed within Projects. The guide will use the project called sbg that was created above.
To visualize the the genome in the genome browser, a sorted BAM file \((na12878\_sorted.bam)\), a binary version of a SAM file, containing sequence alignment data and the respective BAM Index file \((na12878\_sorted.bam.bai)\) should be provided.
From the project sbg dashboard, a new pipeline is created by navigating to Pipelines then Create new pipeline. A Name for the pipeline must be provided and an accompanied short description of the pipeline is optional.
From the pipeline dashboard, we add the following Apps to the Sort SAM pipeline.
- Input File(s): Downloads input files to a local cluster for further processing.
- Picard Sort: Sorts a BAM file. It reads the source BAM file in chunks, sorts them and then merges them. It then builds a BAM Index for a sorted by coordinate BAM file.
- Output File(s): Uploads resulting files from a processing cluster to user storage.
4. Running the Pipeline
Loading Data
Seven Bridges Genomics Platform offers a standalone uploading client to conveniently upload datasets from a local laptop or desktop computer to Seven Bridges.
The Seven Bridges Uploader comes in a 32-bit and 64-bit version and can be downloaded from Files \(\rightarrow\) Add Files \(\rightarrow\) Import From \(\rightarrow\) My Computer
Once the Seven Bridges Uploader has been installed, the data can be uploded by navigating through the Upload button and then selecting the sbg project from the next window before starting the upload.
Running the Pipeline
After the upload is complete, while logged into the Seven Bridges Genomics Platform, under the project sbg, select Sort BAM under Tasks and click on Run this pipeline.
In the next screen, select the \(na12878.bam\) under Input Files then click on Run. Once the task has comleted running, two file \(na12878.sorted.bam\) and \(na12878.sorted.bam.bai\) will appear under Outputs \(\rightarrow\) Output File(s).
5. Visualizing the dataset
By clicking on the file \(na12878.sorted.bam\), a file browser opens up which displays the dataset in the SBG Genome Browser.
