STAMP是一个支持Windows、Linux系统的微生物群落分析软件。与Mothur或QIIME相比,感觉它更小巧、轻便。它没有从测序结果(MiSeq/454)出发直到分析结果的一整套流程,但是它具有从OTU Table出发进行统计分析、作图的能力。借助于scipynumpymatplotlib等Python库的支持,它的分析、绘图能力达到了一个非常令人满意的程度。相应结果基本可以直接在文章中使用。

STAMP is a software package for analyzing taxonomic or metabolic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. Statistical hypothesis tests for pairs of samples or groups of samples is support along with a wide range of exploratory plots. STAMP encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.

它需要的数据有两个:Profile和metadata,分别由两个文件提供。profile是OTU table等核心数据的来源,metadata则包含样品的分组、属性等实验关键设计。


在转换过程中出现了下图所示的UnicodeEncodeError:‘ascii’ codec can’t encode character in position 25-31: ordinal not in range(128)错误。经查是由于文件路径带非ascii字符(中文)造成的。将文件放在全英文的路径中就可以解决这一问题了。

STAMP_unknown error


Chun-Hui Gao is a Research Associate at Huazhong Agricultural University.


Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT. The full source is available at


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gaoch (2016). STAMP: unknown error – Unicode encode error. BIO-SPRING. /post/2016/05/29/2016-05-29-how-to-mending-stamp-unicode-encode-error/

BibTeX citation

  title = "STAMP: unknown error – Unicode encode error",
  author = "gaoch",
  year = "2016",
  journal = "BIO-SPRING",
  note = "/post/2016/05/29/2016-05-29-how-to-mending-stamp-unicode-encode-error/"