20220518_基因组contig与scaffold的N50大小统计

原创

wilson_bit

发布于 2022-05-18 17:37:38

1.4K0

发布于 2022-05-18 17:37:38

文章被收录于专栏：igenomeigenome

20220518_基因组contig与scaffold的N50大小统计

01 assembly_stats软件安装

(base) root@dell-server:/home/# pip install assembly_stats

02 assembly_stats软件使用方法

03 assembly_stats软件统计结果展示

(base) root@dell-server:/home/# assembly_stats  genome.fasta
{
  "Contig Stats": {
    "L10": 1,
    "L20": 3,
    "L30": 6,
    "L40": 9,
    "L50": 13,
    "N10": 14612419,
    "N20": 12596737,
    "N30": 10356262,
    "N40": 7972914,
    "N50": 6039544,
    "gc_content": 32.21673534307239,
    "longest": 15111501,
    "mean": 323711.75977011496,
    "median": 67267.0,
    "sequence_count": 870,
    "shortest": 980,
    "total_bps": 281629231
  },
  "Scaffold Stats": {
    "L10": 0,
    "L20": 1,
    "L30": 2,
    "L40": 3,
    "L50": 5,
    "N10": 45097400,
    "N20": 25348148,
    "N30": 23763320,
    "N40": 21293100,
    "N50": 19542739,
    "gc_content": 32.21673534307239,
    "longest": 45097400,
    "mean": 4024417.5857142857,
    "median": 4077.0,
    "sequence_count": 70,
    "shortest": 1126,
    "total_bps": 281709231
  }
}

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