StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics

Ricardo H. Ramirez-Gonzalez, Richard M. Leggett, Darren Waite, Anil Thanki, Nizar Drou, Mario Caccamo, Robert Davey

Code and Data Abstract

StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, allowing consolidated multi-faceted querying and visualisation of QC and primary analysis data via concise APIs in Java and Perl.

Article

Paper Abstract

We analyzed the relationship between biodiversity and spatial biomass heterogeneity along an ecological succession developed in the laboratory. Periphyton (attached microalgae) biomass spatial patterns at several successional stages were obtained using digital image analysis and at the same time we estimated the species composition and abundance. We show that the spatial pattern was self-similar and as the community developed in an homogeneous environment the pattern is self-organized. To characterize it we estimated the multifractal spectrum of generalized dimensions Dq. Using Dq we analyze the existence of cycles of heterogeneity during succession and the use of the information dimension D1 as an index of successional stage. We did not find cycles but the values of D1 showed an increasing trend as the succession developed and the biomass was higher. D1 was also negatively correlated with Shannon's diversity. Several studies have found this relationship in different ecosystems but here we prove that the community self-organizes and generates its own spatial heterogeneity influencing diversity. If this is confirmed with more experimental and theoretical evidence D1 could be used as an index, easily calculated from remote sensing data, to detect high or low diversity areas.

Ricardo H. Ramirez-Gonzalez, Richard M. Leggett, Darren Waite, Anil Thanki, et al. "StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics." F1000Research.     doi:10.12688/f1000research.2-248.v1. Retrieved 06/24/2019 from researchcompendia.org/compendia/2014.382/

Compendium Type: Published Papers
Primary Research Field: Computer and Information Sciences
Secondary Research Field: Mathematics
Content License: Public Domain Mark
Code License: MIT License

Page Owner

jenn.seiler@gmail.com

created 01/17/2014

modified 01/17/2014

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