Extract barcodes

extract_barcodes.py

Function: To isolate duplex barcodes from paired-end sequence reads and store in FASTQ headers after removal of spacer regions.

(Written for Python 3.5.1)

USAGE:

python3 extract_barcodes.py [–read1 READ1] [–read2 READ2] [–outfile OUTFILE] [–blen BARCODELEN] [–slen SPACERLEN] [–sfilt SPACERFILT]

Arguments:

–read1 READ1	Input FASTQ file for Read 1 (unzipped)
–read2 READ2	Input FASTQ file for Read 2 (unzipped)
–outfile OUTFILE	Output FASTQ files for Read 1 and Read 2 using given filename
–bpattern BPATTERN	Barcode pattern (N = random barcode bases, A|C|G|T = fixed spacer bases)
–blist BARCODELIST	List of correct barcodes

Barcode design:

N = random / barcode bases

A | C | G | T = Fixed spacer bases

e.g. ATNNGT means barcode is flanked by two spacers matching ‘AT’ in front and ‘GT’ behind

Inputs:

1. A FASTQ file containing first-in-pair (Read 1) reads
2. A FASTQ file containing second-in-pair (Read 2) reads

Outputs:

1. A Read 1 FASTQ file with barcodes added to the FASTQ header
2. A Read 2 FASTQ file with barcodes added to the FASTQ header
3. A text file summarizing barcode stats