This DNAqua-Net topical issue edited by the leaders of Working Group 4 (bioinformatics), Diego Fontaneto (Italy) and Alain Franc (France) welcomes submissions on DNA and environmental DNA metabarcoding and metagenomics with a focus on bioinformatic processing and infrastructure. Available bioinformatic pipelines cover all the steps from raw sequence data from massive sequencing to the production of publication-standard graphs and statistical analyses. Yet, such pipelines are usually very general and are not devoted to specific needs: here there is still ample space and opportunity to develop tools and approaches to address and solve some of the weaknesses that still exist for specific applications of metabarcoding. The special issues furthermore welcomes submissions that assess and benchmark infrastructure for processing and storing DNA and eDNA data for large scale monitoring.