The-FBI-Pipeline

Automated End-to-End RNA-Seq Analysis for Fusion Detection and Immune Profiling

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📋 Overview

The-FBI-Pipeline (Fusion, BCR/TCR, Immunogenomics) streamlines paired-end RNA-seq data from raw reads to validated fusion calls and immune repertoire profiles. The modular Bash scripts cover fastp QC, RiboDetector rRNA depletion, STAR-Fusion analysis, merged reporting, and MixCR-based TCR/BCR profiling.

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🚀 Highlights

• Modular steps that run independently or end-to-end
• Reproducible environments via Conda and Docker
• Checkpoint markers (.task.complete) to resume safely
• Consolidated TSV outputs ready for downstream review

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📂 Pipeline Steps

• Step 1 · Quality Control (step-1-quality-control.sh) – fastp trimming, filtering, and interactive QC reports.
• Step 2 · rRNA Removal (step-2-rrna-removal.sh) – RiboDetector deep-learning filter for ribosomal reads.
• Step 3 · Fusion Detection (step-3-fusion-detection.sh) – STAR-Fusion in Docker with FusionInspector validation and coding-effect assessment.
• Step 4 · Merge Results (step-4-merge-fusion-results.sh) – aggregates STAR-Fusion outputs into three master TSV files.
• Step 5 · TCR/BCR Profiling (step-5-tcr-bcr-analysis.sh) – MixCR V(D)J assembly and clonotype summarization.

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🛠️ Quick Start

# Clone repository
git clone https://github.com/LiaoWJLab/FBI.git
cd FBI/code

# Prepare environments (run once)
conda create -n rrna -c bioconda fastp -y
conda create -n ribodetector -c bioconda ribodetector -y
conda create -n mixcr -c bioconda mixcr -y
docker pull trinityctat/starfusion

# Execute steps (edit paths inside scripts beforehand)
bash step-1-quality-control.sh
bash step-2-rrna-removal.sh
bash step-3-fusion-detection.sh
bash step-4-merge-fusion-results.sh
bash step-5-tcr-bcr-analysis.sh

Each script logs progress and writes .task.complete markers so interrupted runs can resume safely.

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📊 Outputs

• 02-fastp/ – cleaned FASTQ files plus fastp HTML/JSON reports
• 03-rribo/ – rRNA-depleted paired reads
• 13-starfusion/ – per-sample STAR-Fusion folders and merged TSV summaries
• 07-mixcr/ – MixCR .vdjca alignments and clonotype tables

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📚 Citations

• Chen et al. 2018 — fastp
• Kang et al. 2022 — RiboDetector
• Haas et al. 2019 — STAR-Fusion
• Bolotin et al. 2015 — MixCR

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👤 Author & Support

Dongqiang Zeng
Southern Medical University
📧 interlaken@smu.edu.cn
🌐 https://github.com/LiaoWJLab/FBI

Report issues or request features at github.com/LiaoWJLab/FBI/issues.

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License: MIT — see LICENSE.
Last Updated: November 15, 2025