{
  "tool": "Trim Galore",
  "schema_version": 1,
  "trim_galore_version": "2.3.0",
  "input_filenames": ["SRR6995998.fastq.gz"],
  "mode": "single-end",
  "read_number": 1,
  "command_line": "trim_galore --cores 20 --quality 20 --length 20 --no_poly_g --adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --adapter CGGAAGAGCACACGTCTGAACTCCAGTCAC --fastqc --fastqc_args --outdir ../output/02-qc-trim/fastqc-trimmed --output_dir ../data/trimmed-reads ../data/raw-reads/SRR6995998.fastq.gz",
  "parameters": {
    "quality_cutoff": 20,
    "adapters": [{"name": "adapter_1", "sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC"}, {"name": "adapter_2", "sequence": "CGGAAGAGCACACGTCTGAACTCCAGTCAC"}],
    "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": false,
    "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": 24792684,
    "reads_with_adapter": 19028308,
    "reads_written": 20934759,
    "reads_too_short": 3857925,
    "reads_too_long": 0,
    "reads_too_many_n": 0,
    "reads_discarded_untrimmed": 0
  },
  "basepair_processing": {
    "total_bp_processed": 2504061084,
    "quality_trimmed_bp": 162739913,
    "total_bp_written": 2032716317
  },
  "adapter_trimming": [
    {
      "name": "adapter_1",
      "sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
      "type": "regular 3'",
      "length": 34,
      "times_trimmed": 13416900,
      "length_distribution": {
        "1": 7486492,
        "2": 556110,
        "3": 215204,
        "4": 143385,
        "5": 117335,
        "6": 111101,
        "7": 108116,
        "8": 85776,
        "9": 91284,
        "10": 88196,
        "11": 62520,
        "12": 73869,
        "13": 63114,
        "14": 58843,
        "15": 58817,
        "16": 54757,
        "17": 57823,
        "18": 57926,
        "19": 27654,
        "20": 40056,
        "21": 37344,
        "22": 33588,
        "23": 30235,
        "24": 29560,
        "25": 27800,
        "26": 23926,
        "27": 23450,
        "28": 24696,
        "29": 19777,
        "30": 20592,
        "31": 13079,
        "32": 18177,
        "33": 18339,
        "34": 14306,
        "35": 11227,
        "36": 11279,
        "37": 11388,
        "38": 9163,
        "39": 7681,
        "40": 8693,
        "41": 9369,
        "42": 9918,
        "43": 6814,
        "44": 7187,
        "45": 6154,
        "46": 5259,
        "47": 4355,
        "48": 4096,
        "49": 3610,
        "50": 4397,
        "51": 6602,
        "52": 5854,
        "53": 3856,
        "54": 4510,
        "55": 4316,
        "56": 6306,
        "57": 9206,
        "58": 10172,
        "59": 6145,
        "60": 10450,
        "61": 13798,
        "62": 34753,
        "63": 58675,
        "64": 20016,
        "65": 25770,
        "66": 54782,
        "67": 178049,
        "68": 391246,
        "69": 1269821,
        "70": 627796,
        "71": 233406,
        "72": 81970,
        "73": 24147,
        "74": 12636,
        "75": 7304,
        "76": 5793,
        "77": 7128,
        "78": 7080,
        "79": 6696,
        "80": 6002,
        "81": 5461,
        "82": 5230,
        "83": 4956,
        "84": 4961,
        "85": 4812,
        "86": 5084,
        "87": 5512,
        "88": 5143,
        "89": 5350,
        "90": 5622,
        "91": 5963,
        "92": 6391,
        "93": 6677,
        "94": 7356,
        "95": 8012,
        "96": 9046,
        "97": 10207,
        "98": 11218,
        "99": 13312,
        "100": 26518,
        "101": 111947
      }
    },
    {
      "name": "adapter_2",
      "sequence": "CGGAAGAGCACACGTCTGAACTCCAGTCAC",
      "type": "regular 3'",
      "length": 30,
      "times_trimmed": 5611408,
      "length_distribution": {
        "1": 4771978,
        "2": 385430,
        "3": 69715,
        "4": 6478,
        "5": 3849,
        "6": 824,
        "7": 239,
        "8": 105,
        "9": 123,
        "10": 157,
        "11": 91,
        "12": 57,
        "13": 94,
        "14": 67,
        "15": 52,
        "16": 53,
        "17": 26,
        "18": 47,
        "19": 85,
        "20": 116,
        "21": 183,
        "22": 269,
        "23": 404,
        "24": 505,
        "25": 708,
        "26": 493,
        "27": 138,
        "28": 183,
        "29": 177,
        "30": 264,
        "31": 106,
        "32": 160,
        "33": 157,
        "34": 161,
        "35": 256,
        "36": 249,
        "37": 260,
        "38": 441,
        "39": 529,
        "40": 432,
        "41": 769,
        "42": 608,
        "43": 454,
        "44": 475,
        "45": 620,
        "46": 560,
        "47": 713,
        "48": 1277,
        "49": 1166,
        "50": 564,
        "51": 736,
        "52": 619,
        "53": 1725,
        "54": 1426,
        "55": 2371,
        "56": 1928,
        "57": 3756,
        "58": 5620,
        "59": 9191,
        "60": 8312,
        "61": 3516,
        "62": 7678,
        "63": 11352,
        "64": 37658,
        "65": 40227,
        "66": 113910,
        "67": 32095,
        "68": 20655,
        "69": 9461,
        "70": 4372,
        "71": 2481,
        "72": 1534,
        "73": 1116,
        "74": 852,
        "75": 661,
        "76": 413,
        "77": 452,
        "78": 487,
        "79": 506,
        "80": 494,
        "81": 488,
        "82": 449,
        "83": 451,
        "84": 504,
        "85": 535,
        "86": 652,
        "87": 668,
        "88": 543,
        "89": 605,
        "90": 681,
        "91": 745,
        "92": 768,
        "93": 837,
        "94": 919,
        "95": 1052,
        "96": 1162,
        "97": 1375,
        "98": 2000,
        "99": 1607,
        "100": 3294,
        "101": 13602
      }
    }
  ],
  "poly_a_trimming": {
    "reads_trimmed": 0,
    "bases_removed": 0
  },
  "poly_g_trimming": {
    "reads_trimmed": 0,
    "bases_removed": 0
  },
  "rrbs": {
    "trimmed_3prime": 0,
    "trimmed_5prime": 0,
    "r2_clipped_5prime": 0
  },
  "pair_validation": null,
  "passthrough": null
}