Abstract
Working with biodiversity data is a computationally intensive process. Numerous applications and services provide options to deal with sequencing and taxonomy data. Professional statistics software are also available to analyze these type of data. However, in-between the two processes there is a huge need to curate biodiversity sample files. Curation involves creating summed abundance values for chosen taxonomy ranks, excluding certain taxa from analysis, and finally merging and downsampling data files. Very few tools, if any, offer a solution to this problem, thus we present Taxamat, a simple data management application that allows for curation of biodiversity data files before they can be imported to other statistics software. Taxamat is a downloadable application for automated curation of biodiversity data featuring taxonomic classification, taxon filtering, sample merging, and downsampling. Input and output files are compatible with most widely used programs. Taxamat is available on the web at http://www.taxamat.com either as a single executable or as an installable package for Microsoft Windows platforms.
Highlights
The widespread availability of next-generation sequencing has led to an incredible growth in the number of biodiversity studies
If any, offer a solution to this problem, we present Taxamat, a simple data management application that allows for curation of biodiversity data files before they can be imported to other statistics software
Taxamat is a downloadable application for automated curation of biodiversity data featuring taxonomic classification, taxon filtering, sample merging, and downsampling
Summary
The widespread availability of next-generation sequencing has led to an incredible growth in the number of biodiversity studies This boom is most prominent in the analysis of microbiome samples originating mainly from soil, water and the commensal flora of humans and animals. There are very few if any tools available that provide a simple solution for data curation, such as taxon filtering, sample data merging, and downsampling These steps are often needed, for example, to exclude host- and food-related sequence data from microbiome samples and to compensate for oversampling when comparing multiple results [13]. Taxamat is a simple tool that allows for the management of biodiversity data by automating high-rank taxon filtering, sample file merging and downsampling of oversampled files
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