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Browsing Research Datasets by Subject "Microbial Ecology"

Browsing Research Datasets by Subject "Microbial Ecology"

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  • (16s) No 0. Raw 16S rRNA fastq data files for Bocas hypoxia study 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    This repository contains the <B>RAW</B> sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number <B>PRJEB36632 (ERP119845)</B>.Raw ...
  • (16s) No 1. DADA2 Workflow (16S rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 1. DADA2 Workflow page of the Bocas Hypoxia study. File names and descriptions:<B>RUN01_read_changes.txt</B>: Tracking changes in read counts (per sample) from the beginning to end of the DADA2 ...
  • (16s) No 2. Data Preparation (16S rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 2. Data Preparation Workflow page of the Bocas Hypoxia study.File names and descriptions:<B>*seq_table.txt, *_tax_table.txt, *_asv.fasta: </B>Sequence tables, taxonomy tables, and ASV fasta files ...
  • (16s) No 3. Diversity (16s rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 3. Diversity Workflow page of the Bocas Hypoxia study.File names and descriptions:<B>16s-water.rdata: </B>contains all variables and phyloseq objects from the pipeline. To see the <B>Objects</B>, ...
  • (16s) No 4. Differentially Abundant ASVs (16s rRNA) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 4. Differentially Abundant ASVs page of the Bocas Hypoxia study.File names and descriptions:<B>da_asvs_pipeline.rdata</B>: contains all variables and objects from the pipeline. To see the Objects, ...
  • Freeman et al., 2020 ISME J isotope data.xlsx 
    Freeman, Christopher; Paul, Valerie J. (The Smithsonian Institution, 2020)
    Stable isotope, photosymbiont abundance (chlorophyll a values), and elemental values (%C, %N, and C:N) for diverse and common Caribbean sponges (Porifera) from the Florida Keys, Belize, Honduras, and Bocas del Toro, ...
  • (mg) No 3. Assembly &amp; Annotations (metagenomes) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    The complete output of the Snakemake workflow describe in the reference linked below. Zipped directories contain the outputs of each step from the workflow. Please note that some information contained in the contigs.db and ...
  • (mg) No 4. Assembly &amp; Annotation Summary (metagenomes) output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Krona plots for Kraken short-read taxonomy and Kaiju contig taxonomy. File names and descriptions as follows:<B>cc-kraken.html</B>: Short-read Kraken Krona plots for site Coral Caye (cc).<B>cr-kraken.html</B>: Short-read ...
  • (mg) No 5. Binning MAGs (metagenomes) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Binning summary data for four collections: 1) <B>CONCOCT_5</B>, the automatic binning, 2) <B>VIRAL_FINAL</B>, the bins after manual refinement deemed to be viral, 3) <B>MICROBIAL_FINAL</B>, the bins after manual refinement ...
  • (mg) No 6. MAG02 Phylogenomic Analysis (metagenome) Output 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Files generated from the pangenomic (<B>01_MAG02_PAN</B>/), phylogenomic (<B>02_MAG02_PHYLOGENOMICS</B>), and 16S rRNA phylogenetic (<B>03_MAG02_16S_rRNA_PHYLOGENETICS</B>) analyses of MAG02. You can use the anvi&#39;o ...
  • No 2. DADA2 Workflow 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Output files from the No 2. DADA2 Workflow page of the Bocas Hypoxia study. File names and descriptions:RUN01_read_changes.txt: Tracking changes in read counts (per sample) from the beginning to end of the DADA2 ...
  • No. 0: Raw 16S rRNA fastq data files for Bocas hypoxia study 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    This repository contains the RAW sequencing data for hypoxia study. Trimmed reads (with primers removed) are deposited at the European Nucleotide Archive, study accession number PRJEB36632 (ERP119845).Raw fastq data files ...
  • Phyloseq workflow for microbial community analysis 
    Scott, Jarrod (The Smithsonian Institution, 2020)
    Complete, fully reproducible phyloseq workflow for 16S rRNA microbiome analysis of the Bocas del Toro hypoxic event. Included are the HTML and Rmarkdown (.Rmd) files plus the output of the DADA2 pipeline in Rdata format ...

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