The objective of this project was to develop open-source software to enable researchers to interact with online databases that are commonly used in the biological sciences. We initiated development of a software package for remote interaction with the European Nucleotide Archive (ENA), which allows researchers to upload nucleotide sequence data and metadata (information about projects and samples that are registered in this database). Additionally, we developed software for quality control of nucleotide sequence data, which allows researchers to check the quality of their data prior to upload and publication. The software developed here has been released as plugins to the QIIME 2 microbiome bioinformatics platform.