Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

By James J Kozich, Sarah L. Westcott, Nielson T. Baxter, S. Highlander, Patrick D. Schloss. Applied and Environmental Microbiology, 2013

6,325 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8aff0a90daf3fd270f851cf4a02025ffc1a546e5

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Citations in the corpus

Perennial grain crop roots and nitrogen management shape soil food webs and soil carbon dynamics (2019, methodology): “A standard mothur pipeline was used to process and analyze bacterial sequence data (Kozich et al., 2013).”
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis (2017, background): “Aggressive filtering and complete overlap between paired-end reads can reduce the rate at which OTU methods misinterpret sequencing artefacts as biological variation (Bokulich et al, 2013; Kozich et al, 2013; Edgar & Flyvbjerg, 2014).”
Bifidobacteria or fiber protect against diet-induced microbiota-mediated colonic mucus deterioration (2017, methodology): “5) using 515F and 806R primers designed for dual indexing (Kozich et al., 2013) and the V2 kit (2×250 bp paired-end reads).”
Ribosomal Database Project: data and tools for high throughput rRNA analysis (2013, methodology): “Using an overall read Q score quality filter to remove low quality sequences, we tested the Assembler against the paired-end assembler and quality filter built into mothur (39), another amplicon analysis program.”
Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment (2016, methodology): “Preprocessed reads from both barcodes were independently analyzed with mothur following the MiSeq standard operating procedure (Kozich et al., 2013).”
Microplastic in Surface Waters of Urban Rivers: Concentration, Sources, and Associated Bacterial Assemblages (2016, methodology): “…column, and downstream water column samples were compared by calculating the Bray–Curtis similarity index for each pair of samples and visualizing the resulting distance matrix using nonmetric multidimensional scaling (nMDS) run within mothur v.1.33.0 (Schloss et al. 2011, Kozich et al. 2013).”