A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements

Description

This repository provides the raw data, analysis code, and results generated during a systematic evaluation of the impact of selected experimental protocol choices on the metagenomic sequencing analysis of microbiome samples. Briefly, a full factorial experimental design was implemented varying biological sample (n=5), operator (n=2), lot (n=2), extraction kit (n=2), 16S variable region (n=2), and reference database (n=3), and the main effects were calculated and compared between parameters (bias effects) and samples (real biological differences). A full description of the effort is provided in the associated publication.

Resources

Name Format Description Link
47 dada2_output%2Fv4_taxa_tab3rdp18.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3rdp18.txt
47 dada2_output%2Fv3_taxa_tab3rdp18.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3rdp18.txt
40 00README.rtf https://data.nist.gov/od/ds/mds2-3092/00README.rtf
47 dada2_output%2Fv4_taxa_tab3Silvav132.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3Silvav132.txt
47 dada2_output%2Fv3_taxa_tab3Silvav132.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3Silvav132.txt
47 dada2_output%2Fv3_taxa_tab3Silvav138.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv3_taxa_tab3Silvav138.txt
47 dada2_output%2Fv4_taxa_tab3Silvav138.txt https://data.nist.gov/od/ds/mds2-3092/dada2_output%2Fv4_taxa_tab3Silvav138.txt
5 ProcessingRawReads.Rmd https://data.nist.gov/od/ds/mds2-3092/ProcessingRawReads.Rmd
5 DataAnalysis.Rmd https://data.nist.gov/od/ds/mds2-3092/DataAnalysis.Rmd
57 raw_reads.zip https://data.nist.gov/od/ds/mds2-3092/raw_reads.zip
0 R code for analysis and figure generation. https://data.nist.gov/od/ds/mds2-3092/resources.zip

Tags

  • microbiome
  • design-of-experiments
  • full-factorial
  • metagenomic-sequencing

Topics

Categories