BCdatabaser

The Reference DB Creator (BCdatabaser) is a pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data.

In a nutshell:

• check inputs for available data at NCBI
• downloads sequences according to parameters
• optional: trims/orients via primers
• adds taxonomy to sequences
• write reports
• web interface or optionally on command line: deposits data publicly at Zenodo.org and assigns a citable DOI

Basic documentation

• Web interface A user-friendly web interface with limited options is available at https://bcdatabaser.molecular.eco. Login via ORCID is mandatory, created databases will be publicly available and assigned a DOI at Zenodo.
• Command line version
• Parameters and Search Details
• Output and file syntax

Further documentation

• Automated post-processing of databases (e.g. additional filters and checks)
• Manual post-processing of databases (e.g. adding sequences or modifying taxonomy)
• Usage with classifiers
• Public deposition

If you use this software, please cite it as below:

Alexander Keller, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, Markus J Ankenbrand, BCdatabaser: on-the-fly reference database creation for (meta-)barcoding, Bioinformatics, Volume 36, Issue 8, 15 April 2020, Pages 2630–2631, https://doi.org/10.1093/bioinformatics/btz960 https://github.com/molbiodiv/bcdatabaser

Please also cite the software used by this pipeline:

• NCBI eutils
• NCBI::Taxonomy module - Förster F. greatfireball/NCBI-Taxonomy v0.90. Zenodo. 2018 Oct 15; http://doi.org/10.5281/zenodo.1462861
• SeqFilter
• dispr
• Krona - Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.