Bioinformatics Guides

BD Rhapsody™ Sequence Analysis Pipeline User's Guide

  • This guide provides detailed instructions on how to set up and run the BD Rhapsody™ Sequence Analysis Pipeline on the Seven Bridges Genomics platform or on a local server installation. This pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported sequencing libraries are those generated by the BD Rhapsody™ assay kits, including: Whole Transcriptome mRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and ATAC-Seq.
  • Doc ID: 23-24580(01)
  • Updated : 06/2024

Latest Version of BD Rhapsody™ Sequence Analysis Pipeline: 2.2.1 

Popular Downloads 

1. Download the GRCh38 Reference (Release 42 (GRCh38.p13)) and GRCm39 Reference (Release M32 (GRCm39)) : for WTA only

2. Download the Human or Mouse References for BD Rhapsody ATAC assay(standalone or with WTA)

3. The BD® AbSeq Antibody FASTA file can be generated from this link

4. All BD Rhapsody™ mRNA Targeted Panel FASTA files are here

5. Download a list of all cell label section whitelists, description of each bead version, python functions to convert between a cell index and the matching sequence here

6. For each bead version, the cell index and matching cell label sequence in FASTA format can be downloaded at these links

New to BD Rhapsody Data Analysis? Get free access to the pipeline via one of two means : 

Cloud-based version

i. Go to
ii. 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.
iii. Click the link in the email invitation and complete the registration. Seven Bridges Genomics displays the dashboard with the demo projects.

Local version

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