Belgrade : Institute of molecular genetics and genetic engineering
Abstract
Environmental DNA (eDNA) is DNA present in an environmental sample, originating from
any biological material released from organisms living in that environment. This DNA can
be isolated, amplified, sequenced, and analyzed in order to examine the taxonomic richness
and abundance of different organism groups in the targeted environment. Methods of
eDNA metabarcoding thus offer a unique opportunity to systematically streamline and
scale-up regular biological assessments across many different environments of interest.
Recently, as a part of the project funded by European structural and investment funds,
Labena d.o.o. company established a modern laboratory in Zagreb focused on the research
and provision of services in the field of eDNA. In collaboration with the Institute Ruđer
Bošković we have been working on developing tests for analysis of water quality based on
the eDNA and, as part of the standardization and optimization of sample-to-results eDNA
analysis process, we developed a custom bioinformatics pipeline to facilitate efficient and
effective eDNA sequencing data analysis.
The pipeline was was written in Bash and utilizes several different algorithms to filter,
trim, merge, denoise and classify targeted eDNA sequences. Python-based scripts which
allow automatically download, filter, and format the data available on various online
platforms were included in the pipeline to facilitate the curation of custom reference
databases needed for taxonomic classification of targeted organism groups. User-friendly
and interactive pipeline report generation, comprised of both wet- and dry-lab step-bystep
sample statistics and graphical representations or the main results, is supported
using Rmarkdown and Plotly and DataTables libraries. The pipeline is containerized in
Docker, allowing for easier environment building and pipeline deployment.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202