Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: 1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; 2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; 3) ensuring complete traceability of the analysis performed; 4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; 5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system (WMS) conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts

The amazing potential of fungi: 50 ways we can exploit fungi industrially

International audienceFungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats thatfungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi havedeveloped numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application inbiotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. Thesearch for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential inlocating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in whichfungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and giveexamples from our own work and the work of other notable researchers. We also provide a flow chart that can be used toconvince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi haveprovided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untappedresource with enormous industrial potentia