colindaven / rs_demultiplex

Simple demultiplexing of FASTQ, one oligo (barcode) at a time

rs_demultiplex

Demultiplex reads in FASTQ format from a FASTQ input file according to an oligo in the first x bases (eg Unique Molecular Identifier, UMI).

• accept oligo of length x, eg 8bp as first command line arg, see examples below

• read FASTQ

• match given oligo exactly to first x bp, eg 8bp, of the read

• write all reads - either default unmodified, i.e. still containing oligo - to standard out

• alternatively, use --remove to trim off the oligo from the read and shorten the fastq qual line too.

See examples below.

Install

1. Install from release (easy)

• download the release file for amd64 architectures
• run: chmod a+x rs_demultiplex
• Finally rs_demultiplex

Install: build:

1. From source: Please first install Rust and Cargo from their website. The clone the repo and build as below.

2. Run one of following for testing (after source code changes):

bash run_test.sh

cargo build --release
cat test.fastq  | target/release/rs_demultiplex --remove --barcode ATGC > ATGC.txt

3. fast prod version - first build a release binary

cargo build --release

4. run on a whole list of barcodes

First populate barcodes.txt with one raw barcode per line (not fasta, raw format). Leave a blank line at the end, else the last barcode might be missed.

bash demux_all.sh

5. Or avoid the bash script, and run things manually

5a. Now pipe in a FASTQ file into the release binary target/release/rs_demultiplex

5b. specify an oligo barcode at the start of a read eg AACTCCGC

5c. reroute standard out output to a FASTQ file (eg AACTCCGC.txt)

# suggested command lines with oligo/barcode supplied as first argument
cat Undetermined_S0_R1.fastq  | target/release/rs_demultiplex --remove --barcode AACTCCGC > AACTCCGC.txt
cat Undetermined_S0_R1.fastq  | target/release/rs_demultiplex --remove --barcode AAGCGGTG > AAGCGGTG.txt

Usage

--
target/release/rs_demultiplex -h
Usage:
  target/release/rs_demultiplex [OPTIONS]


Optional arguments:
  -h,--help             Show this help message and exit
  -b,--barcode BARCODE  Oligo barcode eg AGGATTCC to search for. Any length.
  -r,--remove           Set this to remove barcode sequence and quality from
                        FASTQ file. Default: off