Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD-NCBI-Merger

Abstract

Background Metabarcoding and metagenomic approaches are becoming routine techniquesfor use in biodiversity assessment and in ecological studies. The assignment of taxonomic information to millions of sequences obtained via high-throughput sequencing is challenging, as many DNA reference libraries are lacking information on certain taxonomic groups and can contain erroneous sequences. Combining different reference databases is therefore a promising approach for maximising taxonomic coverage and reliability of results. New information The "BOLD-NCBI-Merger" bash script is introduced, which combines sequence data obtained from the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Database (BOLD) and prepares it for taxonomic assignment with the software MEGAN.