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otutable-utils之计算OTU表汇总信息-otutable_summary和otutab_stats

本文介绍otutable-utils系列的一个小工具:otutab_summary (Github 链接 ), 就是计算OTU表中每个样本的OTU数和tag数,支持未注释的OTU表。

1. 命令行接口

$ otutable_summary
Usage:  otutable_summary <otutab>
version: 0.0.1

2. 命令行接口

otutable_summary OTU_table.txt  >OTU_table.summary.txt

3. 其它实现

3.1 otutab_stats

otutab_stats 是 Usearch 的命令行工具,接口也比较简单

usearch  -otutab_stats  OTU_table.txt   -output     OTU_table.report.txt

该程序对整个OTU表中样本进行统计分析, 示例结果如下:

   1624812  Reads (1.6M)
        27  Samples
      3565  OTUs

     96255  Counts
     44360  Count  =0  (46.1%)
     14975  Count  =1  (15.6%)
     14774  Count >=10 (15.3%)

       504  OTUs found in all samples (14.1%)
       739  OTUs found in 90% of samples (20.7%)
      1808  OTUs found in 50% of samples (50.7%)

Sample sizes: min 48273, lo 59502, med 60943, mean 60178.2, hi 61976, max 62871

本文材料为 BASE (Biostack Applied bioinformatic SEies ) 课程 Linux Command Line Tools for Life Scientists 材料, 版权归 上海逻捷信息科技有限公司 所有.

Last Upate: 2017-11-29 10:18 PM

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