Demultiplex Ion Torrent Reads

readme.md

Demultiplex IonTorrent

(c) 2013 Austin G. Davis-Richardson, LICENSE: MITv3

Requirements

• Ruby 1.9.3 or better (check with ruby --version)
• DNA (sudo gem install dna)

Instructions

./demultiplex_iontorrent.rb reads.fastq

Creates a directory on the desktop called split_by_barcode.

barcodes.csv

demultiplex_iontorrent.rb

#!/usr/bin/env ruby

require 'dna'

# Usage
# 1 - install dna by typing suda gem install dna
# 2 - you need a file called barcodes.csv
#     that contains the barcode,sample_id on each line
# 3 - ruby split.rb reads.fastq
#     this will output files in split_by_barcode/

MIN_READ_LEN = 300
BARCODES = 'barcodes.csv'
OUT_DIR = File.expand_path('~/Desktop/split_by_barcode/')

`mkdir -p #{OUT_DIR}`

barcodes = Hash.new

File.open BARCODES do |handle|
  handle.each do |line|
    line = line.strip.split(',')
    id, barcode = line
    barcodes[barcode] = File.open(File.join(OUT_DIR, "sample_#{id}.fastq"), 'w')
  end
end

File.open ARGV[0] do |handle|
  records = Dna.new(handle)

  records.each do |record|
    bc = record.sequence[0..8]
    handle = barcodes[bc]
    next if handle.nil?

    unless record.sequence.size < MIN_READ_LEN
      # remove barcode from sequence
      record.sequence = record.sequence[7..-1]
      record.quality = record.quality[7..-1]
      handle.puts record
    end
  end
end