BarKeeper – A versatile web framework to assemble, analyze, and manage DNA barcoding data and metadata

Wiechers S; Kösters LM; Quandt D; Borsch T; Wicke S; Müller KF

Abstract

DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high-quality sequences to maximize identification success. BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence- and associated metadata. It is free, open-source, and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location. BarKeeper offers features to collect and manage data and metadata about specimens, taxa, and DNA sequences from Sanger sequencing and High-throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy-based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats. BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error-prone manual steps and enabling efficient collaborative workflows.