BD Rhapsody™ Analysis Pipeline Updates


  • v1.10.1 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:
    • Fixed issue with cell label detection on reads from TCR/BCR, when TCR/BCR libraries were combined with other library types (WTA, Targeted, AbSeq) in a single sequencing index
    • Fixed issue with processing FASTQ files whose filenames end in “fq.gz”
  • v1.10 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:
    • Updated VDJ pipeline with support for full-length contig assembly, improved performance, new metrics, and new output files containing contig sequences

    • Added support for Rhapsody Enhanced Beads, with automatic bead version detection
    • Added option to call putative cells based on AbSeq read counts (for troubleshooting only)
    • Added “Alignment Categories” section to metric summary which provides a breakdown of the types of alignments seen for each library
    • Added separate metric summary files for each sample tag for experiments using BD Single-Cell Multiplexing kits
    • Renamed various metrics in outputs to reflect multi-omics nature of data (Target Type → Bioproduct_Type, Gene/Target → Bioproduct)
    • Added Pct_Read_Pair_Overlap and Median Reads Per cell metric to metric summary
    • Improved support for larger runs on SBG
    • Optimized pipeline metadata handling
    • Improved checking of reference files
  • v1.9.1 of the BD Rhapsody™ Analysis Pipeline for improved WTA Analysis Released:
    • Improved putative cell calling algorithm to reduce overcalling of putative cells in high cell input experiments
    • Updated alignment settings to improve AbSeq mapping when R2 read length is greater than 75 bases
  • v1.9 BD Rhapsody™ Targeted Analysis Pipeline and BD Rhapsody™ WTA Analysis Pipeline Released:
    • Improved FASTQ file pairing - filenames are flexible and pairing is now based on read sequence identifier
    • Optimized pipeline in various steps for memory and storage usage
    • Fixed bugs related to Sample Multiplexing Kit noise and DBEC mean molecule metric
    • BD Rhapsody™ Targeted Analysis Pipeline:
      • Support for BD Rhapsody™ VDJ CDR3 protocol
      • Read and molecule counts for targets from same gene symbol are combined in the output tables
      • Updated Bowtie2 alignment parameters for improved sensitivity
    • BD Rhapsody™ WTA Analysis Pipeline:
      • Updated Pct_Cellular Metrics calculations to match Bioinformatics handbook descriptions
      • Added support for supplemental reference fasta files, which allow alignment to transgenes, like viral RNA or GFP
      • Updated STAR alignment parameters for improved sensitivity