Processing of Illumina MiSeq-generated nifH amplicons from boreal forest moss samples - output after FunGene, CART models and chimera removal

Processing of Illumina MiSeq-generated nifH amplicons from boreal forest moss samples - output after FunGene, CART models and chimera removal

A portion of the nifH (nitrogenase) gene was amplified from twelve samples of boreal forest moss stems (Pleurozium schreberi) from Sweden, using degenerate primers IGK3 and DVV. Sequencing was carried out using the Illumina MiSeq platform, paired-end 300 bp kit. Bioinformatic processing included the...

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Hauptverfasser: Arroniz-Crespo, Maria, Bougoure, Jeremy, Murphy, Daniel V, Cutler, Nick A, Chaput, Dominique, Jones, David L, Souza-Egipsy, Virginia, Ostle, Nick, Wade, Stephen C, Clode, Peta L, DeLuca, Thomas H
Format: Dataset
Sprache:eng
Schlagworte:
Bioinformatics
FOS: Biological sciences
FOS: Computer and information sciences
Microbial Ecology
Microbiology
Terrestrial Ecology
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Zusammenfassung:A portion of the nifH (nitrogenase) gene was amplified from twelve samples of boreal forest moss stems (Pleurozium schreberi) from Sweden, using degenerate primers IGK3 and DVV. Sequencing was carried out using the Illumina MiSeq platform, paired-end 300 bp kit. Bioinformatic processing included the RDP FunGene pipeline and a classification and regressions trees (CART) model (Frank et al. 2016, Environ Microbiol Rep 8:905-916). Output from key steps is available here. Raw data are available on NCBI's SRA, accession numbers SRR5366534-SRR5366545.
DOI:10.6084/m9.figshare.4780684