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ScaleBio Seq Suite

Overview

The ScaleBio Seq Suite: RNA Data Analysis Pipeline is an end-to-end Nextflow workflow designed to process single-cell RNA sequencing data from ScaleBio's single-cell platforms.

Primary Platform: QuantumScale

QuantumScale Single Cell RNA Kit powers the next generation of single-cell analysis:

  • Quantum Barcoding Technology: Consolidates multiple barcoding levels into one streamlined operation, cutting hands-on time by over 75%
  • Ultra-efficient Workflow: Reduces hands-on time without requiring specialized instrumentation
  • Flexible Project Sizes: Easily scales from proof-of-concept studies to massive projects, from 84,000 to 4 million cells
  • High Performance: Achieves cell recovery of 50%-60% or higher while keeping multiplets low (≤4%)
  • ScalePlex Support: Enables higher sample multiplexing through cell labeling
  • Simplified Multiplexing: Easily combines 10 to >9,000 samples or conditions in a single run and eliminates batch effects with ScalePlex
  • Pipeline Compatibility: Requires ScaleRNA v2.0+

Legacy Platform: ScaleRNA v1.1

ScaleRNA v1.1 continues to be supported for existing users:

  • Established Technology: Single-cell RNA sequencing workflow
  • ScalePlex Support: Enables higher sample multiplexing through cell labeling
  • Extended Throughput: Multi-plate merging capabilities for increased throughput
  • Pipeline Compatibility: Works with ScaleRNA v1.4+ (ScalePlex) and v1.6+ (full features)

See our product page for more details: ScaleBio

What This Documentation Covers

🚀 Getting Started

  • System Requirements: 64GB RAM, 12 CPU cores minimum (32GB/6 cores for smaller datasets)
  • Installation Guide: Nextflow setup and dependency management
  • Test Run: Quick validation of your installation
  • Nextflow Basics: Getting to know Nextflow options and configuration
  • FASTQ Generation: Critical information about generating fastq files for all kit configurations
  • v1.6 to v2 Changes: Migration guide for existing users and users switching from ScaleRNA v1.1 to QuantumScale

📁 Input & Configuration

  • Sequencing Reads: Support for BCL files, FASTQ files, and Ultima CRAM files
  • Sample Barcode Table: CSV configuration for sample demultiplexing
  • Analysis Parameters: Comprehensive parameter reference with examples
  • Dependencies: Multiple installation methods (Docker, Singularity, Conda)
  • Reference Genomes: Pre-built genomes and custom genome support

🔄 Pipeline & Analysis

  • Workflow Overview: Step-by-step pipeline execution details
  • Reporting: Comprehensive QC reports and statistics generation
  • ScalePlex Analysis: Advanced multiplexing workflow for sample pooling
  • Cell Calling: Automated cell detection and quality filtering
  • Cell Typing: Optional automated cell type annotation for PBMC samples

📊 Outputs & Results

  • Gene Expression Matrices: Filtered and unfiltered count matrices
  • Quality Control Reports: MultiQC reports, sample-specific QC, and library statistics
  • Barcode Analysis: Demultiplexing results, error rates, and quality metrics
  • Alignment Results: STAR/STARSolo outputs with alignment results
  • ScalePlex Outputs: Sample assignment results and oligo combination statistics

🔧 Advanced Features

  • Custom Reference Genomes: Support for non-standard genome assemblies
  • Extended Throughput: Multi-plate merging for high-throughput workflows
  • Merging Runs: Combining data from multiple sequencing runs
  • Cell Calling Optimization: Customizable thresholds and filtering parameters

❓ Frequently Asked Questions

  • ScaleRNA: Workflow-specific questions and parameter guidance
  • ScalePlex: Multiplexing workflow questions and troubleshooting

Quick Start

For a fast start, you can test the pipeline with sample data or run your own analysis using Nextflow and Docker. Example commands and detailed requirements are provided in the README.md.

To test with sample data, run:

nextflow run ScaleBio/ScaleRna -profile docker -params-file docs/examples/runParams.yml --outDir test

To analyze your own data, use:

nextflow run ScaleBio/ScaleRna -profile docker --samples samples.csv --genome genome.json --runFolder /path/to/run --outDir results

The pipeline requires BCL, FASTQ, or CRAM files, a sample barcode table (CSV), a reference genome (STAR index and annotation), and a Linux system with at least 64GB RAM and 12+ CPUs.

Platform Compatibility

Kit Version Pipeline Version Key Features
QuantumScale v1 v2.0+ QuantumScale support, 32bp i7 cell/bead barcode, ScalePlex support
ScaleRNA v1.1 v1.6+ i5/i7 cell indexing, Extended Throughput, ScalePlex support

QuantumScale Compatibility

Quantum RNA libraries have an entirely different structure from the Single Cell RNA Sequencing Kit v1.1 or v1. With the new design along with the massive increase in dataset size, Quantum library analysis will be restricted to Seq Suite: RNA Data Analysis Pipeline version 2.0.0 or later.

Figure 1: Quantum RNA Library Design

Single Cell RNA Sequencing Kit:

This compatibility requirement for v1.0 and v1.1 is due to different cell indexing configurations between the two kit versions. Cells are still indexed via unique RT Barcodes and Ligation Barcodes, but the position of the third barcode used for combinatorial indexing is different as illustrated Figure 1:

  • Single Cell RNA Sequencing Kit v1.0: the third cell indexing barcode is Index i7 Barcode at the position of Index 1.

  • Single Cell RNA Sequencing Kit v1.1: the third cell indexing barcode is Index i5 Barcode at the position of Index 2.

In addition, changing the cell indexing configuration enables increasing the number of recovered cells from the assay by the usage of multiple Final Distribution Plates from the ScaleBio Single Cell RNA Extended Throughput v1.1 Kit. Version 1.4 and onwards of the Seq Suite: RNA Data Analysis Pipeline supports merging of multiple Final Distribution Plates.

Please review the Extended Throughput section on how to run multiple Final Distribution Plates through the pipeline.

Legal Notices

By purchasing product(s) and downloading the software product(s) of ScaleBio, You accept all of the terms of the License Agreement. If You do not agree to these terms and conditions, You may not use or download any of the software product(s) of ScaleBio.

ScaleBio products may be covered by one or more patents as indicated at: https://scale.bio/legal-notice/

The use of the ScaleBio products described herein is subject to ScaleBio's Terms and Conditions that accompany the product, or such other terms as have been agreed to in writing between ScaleBio and the user.

ScaleBio may make reference to products or services provided by other companies using their brand names or company names solely for the purpose of clarity, and does not assert any ownership rights over those third-party marks or names.

Intended Use

All products and services described herein are intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.

Need Help?

For more information, please contact support@scale.bio or visit our support website.