guide-target-lib-demux

System requirements

Software dependencies and operating systems (including version numbers)

python3 v.3.11.4
biopython v.1.78
python-levenshtein v.0.12.2
Red Hat Enterprise Linux 8

Versions the software has been tested on

python3 v.3.11.4
biopython v.1.78
python-levenshtein v.0.12.2
Red Hat Enterprise Linux 8

Any required non-standard hardware

No

Installation guide

Install python3, biopython, python-levenshtein into a conda environment

Typical install time on a "normal" desktop computer

<1 hour

Demo and instructions for use

Instructions to run on data

Copy demux.py and demuxRef.csv into the directory with a sample FASTQ files for read 1 and read 2. Run the following command

python3 demux.py <sample_R1_001.fastq.gz> <sample_R2_001.fastq.gz>		

Expected output

• Demultiplexed FASTQ files labeled by library member ID, <Nme2_A001_matched.fastq>, <Nme2_A002_matched.fastq>\
• CSV file containing the IDs of matched spacer and barcode sequnces, <output_list.csv>\
• CSV file containing the nucleotide sequences of unmatched spacer and barcode sequences, <no_match_list.csv>

Expected run time for demo on a normal desktop computer

4 hours