Published July 20, 2019
| Version 1.0.0
Dataset
Open
BCdatabaser - its2.viridiplantae.EUgenera.2019-07-19.zip
Creators
- 1. Center for Computational and Theoretical Biology, University of Würzburg, Germany
- 2. Systematic Botany, Justus Liebig Universität Giessen, Germany
Description
Parameters:
- --marker-search-string ITS2 OR 'internal transcribed spacer2'
- --taxonomic-range Viridiplantae
- --sequence-length-filter 100:2000
- --sequences-per-taxon 9
Notes
This dataset was automatically created with data from NCBI using the BCdatabaser tool
Files
its2.viridiplantae.EUgenera.2019-07-19.zip
Files
(211.5 MB)
| Name | Size | Download all |
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md5:1dc58f47282e8936ca42999a9b27000f
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Additional details
Related works
- Cites
- 10.32942/osf.io/cmfu2 (DOI)
- 10.5281/zenodo.1462861 (DOI)
- 10.1186/1471-2105-12-385 (DOI)
References
- 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.