Alternative approaches to improve accessibility, modularity, and reproducibility can be found in open-source workflow systems such as Galaxy. However, these web services work as a black box and are lacking in transparency, flexibility, and even reproducibility as the version and parameters of the tools are not always available. Web services and automated pipelines such as MG-RAST and EBI metagenomics offer solutions to the accessibility issue. These practices raise doubts about a science gold standard: reproducibility. Furthermore, bioinformatics tools are often manually executed and/or patched together with custom scripts. These issues and the involved complexity are prohibiting scientists from participating in the analysis of their own data. In this context, selecting the best tools, configuring them to use the correct parameters and appropriate computational resources, and combining them together in an analysis chain is a complex and error-prone process. In addition, the tools can be complex to use they are command-line tools and may require extensive computational resources (memory, disk space). Designed for amplicon data, both QIIME and Mothur cannot be directly applied to shotgun metagenomics data. For example, to extract taxonomic information with the widely used QIIME or Mothur, at least 10 different tools with at least four parameters each are needed. Each step may require execution of several tools or software. Hence, to extract useful information, a sequenced microbiota sample has to be processed by sophisticated workflows with numerous successive bioinformatics steps. However, meta'omic data exploitation is not trivial due to the large amount of data, their complexity, the incompleteness of reference databases, and the difficulty to find, configure, use, and combine the dedicated bioinformatics tools, etc. These techniques are giving insight into taxonomic profiles and genomic components of microbial communities. The study of microbiota and microbial communities has been facilitated by the evolution of sequencing techniques and the development of metataxonomics, metagenomics, and metatranscriptomics.
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