Dataset Open Access

BCdatabaser - its2.viridiplantae.EUgenera.2019-07-19.zip

Keller, Alexander; Hohlfeld, Sonja C.Y.; Kolter, Andreas; Schultz, Jörg; Gemeinholzer, Birgit; Ankenbrand, Markus J.

Parameters:
  • --marker-search-string ITS2 OR 'internal transcribed spacer2'
  • --taxonomic-range Viridiplantae
  • --sequence-length-filter 100:2000
  • --sequences-per-taxon 9
This dataset was automatically created with data from NCBI using the BCdatabaser tool
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its2.viridiplantae.EUgenera.2019-07-19.zip
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  • Keller et al. (2019) BCdatabaser: on-the-fly reference database creation for (meta-)barcoding. EcoEvoRxiv (2019); https://doi.org/10.32942/osf.io/cmfu2 - https://github.com/molbiodiv/bcdatabaser

  • eutils: Sayers E. E-utilities Quick Start. 2008 Dec 12 [Updated 2018 Oct 24]. In: Entrez Programming Utilities Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK25500/

  • NCBI::Taxonomy: Förster et al. https://github.com/greatfireball/NCBI-Taxonomy - Förster F. greatfireball/NCBI-Taxonomy v0.90. Zenodo. 2018 Oct 15; https://doi.org/10.5281/zenodo.1462861

  • SeqFilter: Hackl et al. https://github.com/BioInf-Wuerzburg/SeqFilter

  • dispr: Cofield et al. https://github.com/douglasgscofield/dispr

  • Krona: Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385.

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