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Cell Ranger VDJ Pipeline Specification

Pipeline Details

  • Name: Cell Ranger VDJ Pipeline
  • Pipeline UUID: c663gjepko4rw1pzrypl384g3hiwfs
  • Version: 1.0.0
  • View Pipeline:

Overview

Cell Ranger VDJ Pipeline is designed for analyzing sequencing data produced from Chromium Single Cell 5' V(D)J libraries. It automates V(D)J sequence assembly, paired clonotype calling, and quality control to provide comprehensive immune repertoire analysis with reliable and reproducible results.

Key Use cases:

  • V(D)J Sequence Assembly: Performs sequence assembly of V(D)J transcripts per cell using Chromium cellular barcodes and UMIs.
  • Clonotype Analysis: Identifies and calls paired clonotypes from single-cell V(D)J sequencing data.
  • CDR3 Sequence Analysis: Extracts and analyzes complementarity-determining region 3 (CDR3) sequences for immune repertoire profiling.

Features

  • Cell Ranger v9.0.0 Integration: Utilizes the latest version of 10x Genomics Cell Ranger for state-of-the-art V(D)J analysis.
  • Automated Quality Control: Implements comprehensive QC steps including FastQC for read quality assessment and MultiQC for consolidated reporting.
  • Loupe V(D)J Browser Compatibility: Generates .vloupe files that can be directly loaded into Loupe V(D)J Browser for interactive visualization.
  • Cellular Barcode Processing: Leverages Chromium cellular barcodes and UMIs for accurate per-cell V(D)J transcript assembly.
  • Comprehensive Reporting: Produces detailed web summary reports and quality metrics for easy interpretation of results.
  • Scalable Processing: Supports configurable CPU and memory allocation for efficient processing of large datasets.

Input/Output Specification

Inputs

Required

Paired-end FASTQ Files (reads)

  • Description: FASTQ files containing raw V(D)J sequencing reads from Chromium Single Cell 5' V(D)J libraries
  • Format: .fastq or .fastq.gz
  • Requirements: Paired-end reads (R1 and R2) with proper naming convention for Cell Ranger processing

Reference Genome

  • Description: V(D)J reference genome for sequence alignment and assembly
  • Format: Cell Ranger compatible reference directory
  • Requirements: Must be compatible with Cell Ranger v9.0.0

Mate Parameter

  • Description: Specification of read pairing configuration
  • Format: String parameter
  • Value: "pair" for paired-end sequencing data

Outputs

Reported Outputs

  • Cell Ranger VDJ Output Directory:
  • Description: Complete Cell Ranger VDJ analysis results including clonotype information, consensus annotations, and filtered data
  • Format: Directory structure with multiple file types (.csv, .json, .fasta, .vloupe)
  • Location: {sample_name}_outs/

  • Visualization App: Loupe V(D)J Browser

  • Web Summary Report:

  • Description: Interactive HTML report with key metrics, quality control information, and analysis summary
  • Format: .html
  • Location: {sample_name}_web_summary.html
  • Visualization App: Web browser

Supporting Outputs

  • FastQC Quality Reports:
  • Description: Individual quality control reports for input FASTQ files
  • Format: .html and .zip files

  • Location: FastQC output directory

  • MultiQC Summary Report:

  • Description: Consolidated quality control report combining all QC metrics from the pipeline
  • Format: .html
  • Location: MultiQC output directory
  • Visualization App: Web browser

Associated Processes

References & Additional Documentation

  • 10x Genomics Documentation: Cell Ranger VDJ Analysis
  • Cell Ranger Version: v9.0.0
  • Supported Library Types: Chromium Single Cell 5' V(D)J libraries