{
  "tool": "Trim Galore",
  "schema_version": 1,
  "trim_galore_version": "2.3.0",
  "input_filenames": ["SRR6995995.fastq.gz"],
  "mode": "single-end",
  "read_number": 1,
  "command_line": "trim_galore --cores 20 --quality 20 --length 20 --fastqc --fastqc_args --outdir ../output/02-qc-trim/fastqc-trimmed --output_dir ../data/trimmed-reads ../data/raw-reads/SRR6995995.fastq.gz",
  "parameters": {
    "quality_cutoff": 20,
    "adapters": [{"name": "Illumina", "sequence": "AGATCGGAAGAGC"}],
    "adapters_r2": [],
    "times": 1,
    "error_rate": 0.1,
    "stringency": 1,
    "length_cutoff": 20,
    "max_length": null,
    "phred_encoding": 33,
    "trim_n": false,
    "nextseq": false,
    "rrbs": false,
    "non_directional": false,
    "poly_a": false,
    "poly_g": true,
    "clip_r1": null,
    "clip_r2": null,
    "three_prime_clip_r1": null,
    "three_prime_clip_r2": null,
    "max_n": null,
    "discard_untrimmed": false,
    "consider_already_trimmed": null
  },
  "read_processing": {
    "total_reads": 39780221,
    "reads_with_adapter": 23668832,
    "reads_written": 33297145,
    "reads_too_short": 6483076,
    "reads_too_long": 0,
    "reads_too_many_n": 0,
    "reads_discarded_untrimmed": 0
  },
  "basepair_processing": {
    "total_bp_processed": 4017802321,
    "quality_trimmed_bp": 316184920,
    "total_bp_written": 3165289825
  },
  "adapter_trimming": [
    {
      "name": "Illumina",
      "sequence": "AGATCGGAAGAGC",
      "type": "regular 3'",
      "length": 13,
      "times_trimmed": 23668832,
      "length_distribution": {
        "1": 11462116,
        "2": 913639,
        "3": 452031,
        "4": 350618,
        "5": 306933,
        "6": 287673,
        "7": 281622,
        "8": 223594,
        "9": 240111,
        "10": 227277,
        "11": 163863,
        "12": 191866,
        "13": 162016,
        "14": 154332,
        "15": 155092,
        "16": 135444,
        "17": 148906,
        "18": 139969,
        "19": 77237,
        "20": 100751,
        "21": 92710,
        "22": 92332,
        "23": 71942,
        "24": 71831,
        "25": 70031,
        "26": 59001,
        "27": 60092,
        "28": 69170,
        "29": 44476,
        "30": 56054,
        "31": 26700,
        "32": 44622,
        "33": 37960,
        "34": 33786,
        "35": 32078,
        "36": 29446,
        "37": 24823,
        "38": 22225,
        "39": 18967,
        "40": 18640,
        "41": 17506,
        "42": 18111,
        "43": 14856,
        "44": 15499,
        "45": 14325,
        "46": 11856,
        "47": 10329,
        "48": 9714,
        "49": 9605,
        "50": 9484,
        "51": 14034,
        "52": 13280,
        "53": 8932,
        "54": 9882,
        "55": 9119,
        "56": 13038,
        "57": 18891,
        "58": 20514,
        "59": 11921,
        "60": 19122,
        "61": 23840,
        "62": 75716,
        "63": 106484,
        "64": 28951,
        "65": 37257,
        "66": 83778,
        "67": 294897,
        "68": 680706,
        "69": 2318979,
        "70": 1329345,
        "71": 473970,
        "72": 166570,
        "73": 46778,
        "74": 24045,
        "75": 13890,
        "76": 11132,
        "77": 15031,
        "78": 14608,
        "79": 13595,
        "80": 11887,
        "81": 10350,
        "82": 10109,
        "83": 9110,
        "84": 8688,
        "85": 8905,
        "86": 9256,
        "87": 9870,
        "88": 9386,
        "89": 9536,
        "90": 10143,
        "91": 10789,
        "92": 11390,
        "93": 11919,
        "94": 13136,
        "95": 14072,
        "96": 16424,
        "97": 18075,
        "98": 20232,
        "99": 23227,
        "100": 46740,
        "101": 194022
      }
    }
  ],
  "poly_a_trimming": {
    "reads_trimmed": 0,
    "bases_removed": 0
  },
  "poly_g_trimming": {
    "reads_trimmed": 431609,
    "bases_removed": 1694834
  },
  "rrbs": {
    "trimmed_3prime": 0,
    "trimmed_5prime": 0,
    "r2_clipped_5prime": 0
  },
  "pair_validation": null,
  "passthrough": null
}
