RM-seq
======

Usage
=====

::

    RM-seq.pl [options] --R1 R1.fq.gz --R2 R2.fq.gz --refnuc FASTA --refprot FASTA --outdir DIR --barlen NN
      --help          This help.
      --debug!        Debug info (default '0').
      --R1=s          Read 1 FASTQ (default '').
      --R2=s          Read 2 FASTQ (default '').
      --refnuc=s      Reference gene that will be used for premapping filtering (fasta) (default '').
      --refprot=s     Reference protein that will be use for annotating variants (fasta) (default '').
      --outdir=s      Output folder (default '').
      --force!        Force overwite of existing (default '0').
      --barlen=i      Length of barcode (default '16').
      --minfreq=i     Minimum barcode frequency to keep (default '5').
      --cpus=i        Number of CPUs to use (default '1').
      --minsize=i     Minimum ORF size in bp used when annotating variants (default '200').
      --wsize=i       Word-size option to pass to diffseq for comparison with reference sequence (default '5').
      --subsample=i   Only examine this many reads (default '0').
      --keepfiles!    Do not delete intermediate files (default '0').

