rmseq 0.0.2b0

RM-seq is a bioinformatics tool for for assessing resistance mutations from PE short-reads.

# 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').
```