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Cumulus Tool on Feature Barcoding

A fast C++ tool to extract feature-count matrix from sequence reads in FASTQ files. It is used by Cumulus for feature-count matrix generation of cell hashing, nucleus hashing, CITE-Seq and Perturb-seq protocols, using either 10x Genomics V2 or V3 chemistry.

Installation

The installation has been tested on Debian and Ubuntu Linux.

  1. Install dependency packages:
sudo apt install build-essential git libboost-iostreams-dev
  1. Check out this repository via Git:
git clone https://github.com/lilab-bcb/cumulus_feature_barcoding.git
  1. Enter the directory and compile:
cd cumulus_feature_barcoding
make all
  1. Now you'll have an executable named generate_count_matrix_ADTs inside your folder. Type
./generate_count_matrix_ADTs

to see its usage.

Compile on Mac OS

  1. Install boost using homebrew
brew install boost
  1. Set up environment variables
export CPATH=/usr/local/opt/boost/include
export LIBRARY_PATH=/usr/local/opt/boost/lib
  1. Compile
cd cumulus_feature_barcoding
make all

Usage