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barcoding

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.

Data

The dataset (in t/data/) was prepared with two barcodes for illustrative purposes.

Scripts

Scripts can be found in the bin/ subdirectory. Note: Run the script (split_barcodes.pl) as-is for now. Nothing else has been modified.

Prerequisites

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)