BD Rhapsody™ Sequence Analysis Pipeline

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Overview

The BD Rhapsody^™Sequence Analysis Pipeline is a versatile tool that offers the flexibility to run your bioinformatics analysis on either a Seven Bridges cloud-based platform or on a local installation.

The BD Rhapsody^™Sequence Analysis Pipeline:

Provides a primary analysis of single-cell multiomics data by leveraging cutting-edge algorithms to deliver fast results and deep insights.
Utilizes an intuitive user interface via a cloud-based platform and is easy to use, regardless of the computational expertise of the user.
Offers the ability to choose between cloud-based or local installation options and affords maximum convenience and accessibility for single-cell multiomics data analysis.
Provides broad compatibility of output data with downstream analysis tools such as Seurat and Scanpy.

Pipeline Overview

After sequencing, the pipeline takes input from FASTQ files, a reference (Targeted panel or WTA genome archive), an AbSeq reference (if required), and a supplemental reference (if required), using those to generate molecule counts per cell and metrics about the pipleline run.

Features

Free : Upload raw data, run the pipeline and download results from the cloud for free
Fast: Less than 3 hours to process 1 billion reads
Simple: One consolidated pipeline for BD Rhapsody^™ Whole Transcriptome Analysis Amplification Kit, BD Rhapsody^™ Targeted mRNA Kits, BD Rhapsody^™ TCR/BCR Next Multiomic Assays and BD Rhapsody^™ ATAC-Seq Assays

Release notes

v2.2.1 BD Rhapsody™ Sequence Analysis Pipeline

June 05, 2024

Additions

Support for MGI sequencer FASTQ read header and file names
For TCR/BCR assay, new output of a compressed bundle of PNG images showing the per chain VDJ DBEC algorithm thresholds
Long read support - added new pipeline parameter for enabling support for long R2 reads (>650 bp) - default is to auto-detect long or short reads

Updates

Ability to customize STAR and BWA-MEM2 alignment parameters, enabled on Seven Bridges and local runs

Fixes

Failures that could occur with MGI sequencer FASTQ files in the QualCLAlign or AlignmentAnalysis nodes
Failure caused by VDJ AssembleAndAnnotate node – Argument list too long
Failure caused by MergeBam node – Argument list too long
PhiX aligned reads could incorrectly be counted as targeted mRNA reads when using a targeted panel (usually these are already removed during FASTQ generation)

v2.2 BD Rhapsody™ Sequence Analysis Pipeline

April 19, 2024

Additions

Added support for ATAC-Seq Assay and Multiomic ATAC-Seq Assay (WTA+ATAC-Seq)
Added ability to customize STAR alignment parameters

Updates

Updated the immune cell type classifier to be more lenient in the percentage of bioproducts required to run
Updated TCR BCR annotation software IGBlast to version 1.22
Updated TCR BCR annotation to IMGT release 202349-3 (12-06-2023)
Updated bead version detection

Fixes

Fixed error in dimensionality reduction when zero variable genes are found due to very sparse data

Get Free Access to the Pipeline

Cloud-Based Version

Go to Velsera.com
Click Request Access. In the request access window, enter your email address to receive an email invitation to the Seven Bridges Genomics platform within 24 hours.
Click the link in the email invitation and complete the registration. Seven Bridges Genomics displays the dashboard with the demo projects.

Local Version

Go to bitbucket.org/CRSwDev/cwl. If necessary, create a Bitbucket account.
In the left pane, click Downloads > Download Repository. The CWL and YML files will download.
Unzip the archive. Each folder within the archive is named after the pipeline version to which it corresponds.

Resources

User's Guide

BD Rhapsody™ Sequence Analysis Pipeline User's Guide