Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger

Jan-Niklas Macher; Till-Hendrik Macher; Florian Leese

doi:10.3897/mbmg.1.22262

Software Description

Metabarcoding and Metagenomics 1: e22262
https://doi.org/10.3897/mbmg.1.22262 (15 Dec 2017)

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Luna M. van der Loos, Reindert Nijland (2021)
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Molecular Ecology 30: 3270.

DOI: 10.1111/mec.15592

Kaiying Liu, Hongyue Sun, Xin Zhao, Chaoqun Wang, Changting An, Ang Li, Shufang Liu, Zhimeng Zhuang (2024)
DNA barcoding, identification, and validation of the pufferfish (Order: Tetraodontiformes) in China coastal waters. Ecology and Evolution 14: .

DOI: 10.1002/ece3.10944

Emese Meglécz (2023)
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline. Molecular Ecology Resources 23: 933.

DOI: 10.1111/1755-0998.13756

Raphaël Hebert, Emese Meglécz (2022)
NSDPY: A python package to download DNA sequences from NCBI. SoftwareX 18: 101038.

DOI: 10.1016/j.softx.2022.101038

Connor M. French, Laura D. Bertola, Ana C. Carnaval, Evan P. Economo, Jamie M. Kass, David J. Lohman, Katharine A. Marske, Rudolf Meier, Isaac Overcast, Andrew J. Rominger, Phillip P. A. Staniczenko, Michael J. Hickerson (2023)
Global determinants of insect mitochondrial genetic diversity. Nature Communications 14: .

DOI: 10.1038/s41467-023-40936-0

Laura A. Hardulak, Jérôme Morinière, Axel Hausmann, Lars Hendrich, Stefan Schmidt, Dieter Doczkal, Jörg Müller, Paul D. N. Hebert, Gerhard Haszprunar (2020)
DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species. Molecular Ecology Resources 20: 1542.

DOI: 10.1111/1755-0998.13212

Teresita M. Porter, Mehrdad Hajibabaei (2020)
Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis. Frontiers in Ecology and Evolution 8: .

DOI: 10.3389/fevo.2020.00248

Niklas W. Noll, Christoph Scherber, Livia Schäffler (2023)
taxalogue: a toolkit to create comprehensive CO1 reference databases. PeerJ 11: e16253.

DOI: 10.7717/peerj.16253

Teresita M. Porter, Mehrdad Hajibabaei, Wolfgang Arthofer (2018)
Over 2.5 million COI sequences in GenBank and growing. PLOS ONE 13: e0200177.

DOI: 10.1371/journal.pone.0200177

Kelly A. Meiklejohn, Natalie Damaso, James M. Robertson, Sebastian D. Fugmann (2019)
Assessment of BOLD and GenBank – Their accuracy and reliability for the identification of biological materials. PLOS ONE 14: e0217084.

DOI: 10.1371/journal.pone.0217084

Romy Gielings, Maria Fais, Diego Fontaneto, Simon Creer, Filipe Oliveira Costa, Willem Renema, Jan-Niklas Macher (2021)
DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review. Frontiers in Marine Science 8: .

DOI: 10.3389/fmars.2021.730063

Vanessa Arranz, William S. Pearman, J. David Aguirre, Libby Liggins (2020)
MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. Scientific Data 7: .

DOI: 10.1038/s41597-020-0549-9

Elizabeth Andruszkiewicz Allan, Michelle H. DiBenedetto, Andone C. Lavery, Annette F. Govindarajan, Weifeng G. Zhang (2021)
Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean. Scientific Reports 11: .

DOI: 10.1038/s41598-021-00288-5

Francesco Zangaro, Benedetta Saccomanno, Eftychia Tzafesta, Fabio Bozzeda, Valeria Specchia, Maurizio Pinna (2021)
Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA. NeoBiota 70: 151.

DOI: 10.3897/neobiota.70.71862

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