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Welcome to BroCOLI’s documentation!

Introduction

BroCOLI (Bron-Kerbosch calibrator of Long-read Isoform) leverages BK algorithms for transcript identification and quantification from long-read RNA-Seq data, supporting bulk, single-cell and spatial applications, while maintaining low memory usage and fast performance for large-scale datasets.

Requirements

BroCOLI requires a C++11 compatible compiler (e.g., g++ 4.8 or later).

🚀 Installation

BroCOLI is available on BroCOLI GitHub.

BroCOLI can be installed via the source code:

download and install
git clone https://github.com/gyjames/BroCOLI.git
cd BroCOLI
sh build.sh
Once compiled, two executables ( BroCOLI_bulk and BroCOLI_sc ) will appear in the BroCOLI folder. You can use either the -h (--help) argument or the demo data to verify if the program runs successfully.
help
./BroCOLI_bulk -h
./BroCOLI_sc -h

✨ Supported sequencing data

  • ONT cDNA/ONT dRNA
  • PacBio
  • 10x3v3
  • 10X Visium
  • MAGIC-seq

Supported reference data

  • Reference genome should be provided in FASTA format.
  • Reference annotation is not mandatory, but providing it will yield better results. Please provide it in GTF format.

Usage

📝 Go to Tutorials

🎉 Citation

Reference

  1. C++11 ThreadPool
  2. Li H. Minimap2: pairwise alignment for nucleotide sequences[J]. Bioinformatics, 2018, 34(18): 3094-3100.
  3. Flexiplex

Feedback and bug reports

If you come across any issues or have suggestions, please feel free to contact Wei Pan (weipan4396@gmail.com), or open an issue if you find bugs.