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

2. Check out this repository via Git:

git clone https://github.com/lilab-bcb/cumulus_feature_barcoding.git

3. Enter the directory and compile:

cd cumulus_feature_barcoding
make all

4. 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

2. Set up environment variables

export CPATH=/usr/local/opt/boost/include
export LIBRARY_PATH=/usr/local/opt/boost/lib

3. Compile

cd cumulus_feature_barcoding
make all

Usage