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DNABarcodes specifications

Information


Unique identifier OMICS_14651
Name DNABarcodes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
parallel, Matrix, BiocStyle, rmarkdown, knitr, BH, Rcpp(>=0.11.2)
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Tilo Buschmann

Publication for DNABarcodes

DNABarcodes citations

 (6)
library_books

Quartz Seq2: a high throughput single cell RNA sequencing method that effectively uses limited sequence reads

2018
Genome Biol
PMCID: 5845169
PMID: 29523163
DOI: 10.1186/s13059-018-1407-3

[…] The selection of 384 or 1536 sequences for v3.1 and v3.2 barcode primer sets was performed as described below. First, 1582 or 4714 candidate sequences were created using the DNABarcodes package of R Bioconductor for the v3.1 set with 14-mer and the v3.2 set with 15-mer, respectively (version 1.0.0). To reduce the loss of reads converted into UMI counts, we applied the Seq […]

library_books

Large scale DNA Barcode Library Generation for Biomolecule Identification in High throughput Screens

2017
Sci Rep
PMCID: 5654825
PMID: 29066821
DOI: 10.1038/s41598-017-12825-2

[…] vely. More sophisticated barcode library design methods based on error-correcting codes have been proposed for correcting substitutions and indel errors inherent to NGS sequencing technologies,–. The DNABarcodes R package implements the error-correcting codes based generation method of Buschmann and Bystrykh. The libraries described in the package manual contain from tens to hundreds of barcodes. […]

library_books

Two new Megalothorax species of the minimus group (Collembola, Neelidae)

2016
Zookeys
PMCID: 4740829
PMID: 26877679
DOI: 10.3897/zookeys.554.6069

[…] gth ones (C_LepFolF/C_LepFolR) (Ivanova - published on http://www.boldsystems.org). The standard PCR reaction protocol of the Canadian Center for DNA Barcoding was used for amplifications (http://www.dnabarcodes2011.org/conference/preconference/CCDB-Amplification-animals.pdf), and products were checked on a 2% E-gel 96Agarose (Invitrogen). Unpurified PCR amplicons were sequenced in both directions […]

library_books

DNA Barcoding as an Effective Tool in Improving a Digital Plant Identification System: A Case Study for the Area of Mt. Valerio, Trieste (NE Italy)

2012
PLoS One
PMCID: 3438168
PMID: 22970123
DOI: 10.1371/journal.pone.0043256

[…] idase subunit 1) as a standard region. However, as far as plants are concerned, there was no strong consensus on which DNA regions should be used (Fourth International Barcode of Life Conference, www.dnabarcodes2011.org). The Plant Working Group of the Consortium for the Barcode of Life (http://www.barcoding.si.edu/plant_working_group.html) suggested the use of two plastidial coding regions, the r […]

library_books

Barcoding Life to Conserve Biological Diversity: Beyond the Taxonomic Imperative

2010
PLoS Biol
PMCID: 2903590
PMID: 20644709
DOI: 10.1371/journal.pbio.1000417

[…] efforts. However, iBOL recognizes that such a strategy is not sustainable as the endeavor continues to grow. For this reason, iBOL together with CBOL asked experts at a recent conference (http://www.dnabarcodes2009.org/) to draft position papers about access and benefit sharing as they relate to the iBOL project. Summaries of three key perspectives, relating barcoding to the Convention on Biologi […]

library_books

Transcriptome screen for fast evolving genes by Inter Specific Selective Hybridization (ISSH)

2010
BMC Genomics
PMCID: 2838844
PMID: 20175901
DOI: 10.1186/1471-2164-11-126

[…] ng and non-coding DNA markers, we calculated the sequence divergence of the mitochondrial cytochrome oxydase I gene (COI), used by the Barcode of Life Initiative for characterizing species http://www.dnabarcodes.org/, and the two introns of the reticulon 4 (RTN4) gene, used to infer fish phylogenies at the specific level []. Most of the tentatively annotated transcripts display higher sequence div […]

Citations

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DNABarcodes institution(s)
Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
DNABarcodes funding source(s)
This work was supported by the European Commission project EuroSyStem (200270) and by the RIBOLUTION project of Fraunhofer-Zukunftsstiftung.

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