process_radtags -p in_dir [--paired [--interleaved]] [-b barcode_file] -o out_dir -e enz [-c] [-q] [-r] [-t len]
process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [-c] [-q] [-r] [-t len]
process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [-c] [-q] [-r] [-t len]

  p: path to a directory of files.
  P,--paired: files contained within the directory are paired.
  I,--interleaved: specify that the paired-end reads are interleaved in single files.
  i: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to).
  b: path to a file containing barcodes for this run, omit to ignore any barcoding.
  o: path to output the processed files.
  f: path to the input file if processing single-end sequences.
  1: first input file in a set of paired-end sequences.
  2: second input file in a set of paired-end sequences.
  c,--clean: clean data, remove any read with an uncalled base.
  q,--quality: discard reads with low quality scores.
  r,--rescue: rescue barcodes and RAD-Tags.
  t: truncate final read length to this value.
  D: capture discarded reads to a file.
  E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5).
  w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).
  s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).
  y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type).

  Barcode options:
    --inline-null:   barcode is inline with sequence, occurs only on single-end read (default).
    --index-null:    barcode is provded in FASTQ header (Illumina i5 or i7 read).
    --null-index:    barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).
    --inline-inline: barcode is inline with sequence, occurs on single and paired-end read.
    --index-index:   barcode is provded in FASTQ header (Illumina i5 and i7 reads).
    --inline-index:  barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read).
    --index-inline:  barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data).

  Restriction enzyme options:
    -e <enz>, --renz-1 <enz>: provide the restriction enzyme used (cut site occurs on single-end read)
    --renz-2 <enz>: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).
    Currently supported enzymes include:
      'aciI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 'bamHI', 
      'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 'btgI', 
      'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 'ecoRV', 
      'ecoT22I', 'haeIII', 'hinP1I', 'hindIII', 'hpaII', 'hpyCH4IV', 'kpnI', 'mluCI', 
      'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 'nheI', 'nlaIII', 'notI', 
      'nsiI', 'nspI', 'pacI', 'pspXI', 'pstI', 'rsaI', 'sacI', 'sau3AI', 
      'sbfI', 'sexAI', 'sgrAI', 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI'
      

  Protocol-specific options:
    --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads.

  Adapter options:
    --adapter-1 <sequence>: provide adaptor sequence that may occur on the single-end read for filtering.
    --adapter-2 <sequence>: provide adaptor sequence that may occur on the paired-read for filtering.
      --adapter-mm <mismatches>: number of mismatches allowed in the adapter sequence.

  Output options:
    --retain-header: retain unmodified FASTQ headers in the output.
    --merge: if no barcodes are specified, merge all input files into a single output file.

  Advanced options:
    --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.
    --disable-rad-check: disable checking if the RAD site is intact.
    --len-limit <limit>: specify a minimum sequence length (useful if your data has already been trimmed).
    --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1).
    --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1).

分析：

• 输入支持目录和文件两种方式
  • 目录：通过-P/--paired 指定是否双端数据
  • 文件：单端-f指定文件；双端-1\-2指定R1和R2文件
• 可选参数 [-c] [-q] [-r] [-t len]
  • -c 表示数据清洗时去除表示为N的碱基，
  • -q 表示数据清理时要去除低质量碱基 ,
  • -r 表示要抢救下barcode和RAD-tag。
• 单选参数：
  • barcode 类型 -b
  • 建库所用的限制性内切酶 -e, --renz-1\--renz-2
  • 质量分数编码 -E,有默认值 phred33