This is a demultiplexing script for Nanopore-generated fastq files. It was forked from ONT, and I added parallel processing and several other options
Instructions:
split_barcodes.pl --barcodes ONT_NativeBarcodes.fasta --threads 12 --stringency 6 allreads.fastq
--barcodes FASTA file of Barcodes
--threads Threads to use
--stringency Edit distance to tolerate (default:6)
--verbose Extra information on the reads
--require_both Require both ends to have a barcode
--enforce_orientation Require each barcode to be the expected orientation
--check_hybrid Check if there are additional barcodes in middle of read
(throws out if this is a hybrid read)
Currently, the script expects the fastq file (or symlink) to be in the working directory.
This repository is part of the ONT Barcoding Protocol for amplicons.
The dataset (in t/data/) was prepared with two barcodes for illustrative purposes.
Scripts can be found in the bin/ subdirectory. Note: Run the script (split_barcodes.pl) as-is for now. Nothing else has been modified.
The main prerequisites are listed below, with a complete list available in Build.PL:
- Bio::Perl
- Text::LevenshteinXS
- Readonly
All should be available from CPAN (UNIX/Strawberry systems: "cpan ") or PPD (for ActivePerl)