BCdatabaser - rbcl.viridiplantae.CoffeaCanariumTheobroma.2019-07-15.zip

Published July 15, 2019 | Version 1.0.0

Dataset Open

1. Center for Computational and Theoretical Biology, University of Würzburg, Germany
2. Systematic Botany, Justus Liebig Universität Giessen, Germany

Parameters:

--marker-search-string rbcL OR 'ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit'
--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

Name	Size	Download all
rbcl.viridiplantae.CoffeaCanariumTheobroma.2019-07-15.zip md5:c39166146094db5664ab00853f49fff1	799.8 MB	Preview Download

Cites: 10.32942/osf.io/cmfu2 (DOI); 10.5281/zenodo.1462861 (DOI); 10.1186/1471-2105-12-385 (DOI)

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.