$ rnftools merge -h

usage: rnftools merge [-h] -i inp [inp ...] -m mode -o out

todo

optional arguments:
  -h, --help        show this help message and exit
  -i inp [inp ...]  input FASTQ files
  -m mode           mode for mergeing files (single-end / paired-end-bwa / paired-end-bfast)
  -o out            output prefix

Source RNF-FASTQ files should satisfy the following conditions:
   1) Each file contains only reads corresponding to one genome (with the 
      same genome id).
   2) All files contain reads of the same type (single-end / paired-end).
   3) Reads with more reads per tuple (e.g., paired-end) have '/1', etc.
      in suffix (for identification of nb of read).
