This is a fork of the original repo. I might be taking this tool into a different direction to what was originally intended

sabre

A cellular barcode demultiplexing tool of FASTQ files

Content

• Install
• Quick start
• Usage

Install

git clone https://github.com/serine/sabre
cd src
make

Quick start

sabre -f MultiplexRNASeq_S1_R1_001.fastq.gz \
      -r MultiplexRNASeq_S1_R2_001.fastq.gz \
      -b barcodes.txt \
      -c \
      -u \
      -m 2 \
      -l 10 \
      -a 1 \
      -s sabre.txt \
      -t 12

Usage

This tool is under development and this is very much an alpha version In it's current form the tool is highly customised a particular multiplexing protocol

Cellular barcodes

In order to demultiplex the use needs to provide barcodes.txt file, which is three column tab delimited file

sample_name group barcode

currently group is semi-redundant column, it there for a feature that in the development. for most use cases group can equals to barcode

e.g

cntr_rep1    TAAGGCGA        TAAGGCGA
cntr_rep2    CGTACTAG        CGTACTAG
treat_rep1   AGGCAGAA        AGGCAGAA
treat_rep2   TCCTGAGC        TCCTGAGC