NGSのサンプルデータっぽい感じで，fastaから適当に短い配列取ってきてfastqにするスクリプト

rand_fastq.rb

#/usr/bin/env ruby

# usage:
# ruby rand_fastq.rb hoge.fasta > random.fastq

require 'bio'

genome = ""
read_length = 100
read_count = 10000000

Bio::FlatFile.open(Bio::FastaFormat,ARGV[0]).each do |e|
  genome << e.naseq.gsub(/n/,"")
end

random_start = Array.new( read_count ){ rand genome.length - read_length}

random_start.each_with_index do |r,i|
  seq = Bio::Sequence.new(genome[r, read_length].upcase)
  puts seq.output(:fastq, :title=> "random_"+i.to_s, :width => read_length)
end