This repository provides analysis code and results produced during evaluation of metagenomic sequencing (MGS) data collected through the Mosaic Standards Challenge. The Mosaic Standards Challenge asked participating laboratories analyze the same set of 7 samples using their own favored MGS laboratory methods. Each lab submitted their raw sequencing results and protocol information. The resulting MGS data was analyzed through a common bioinformatic pipeline and then evaluated to determine the effects of methodological choices.

This repository provides analysis code and results produced during evaluation of metagenomic sequencing (MGS) data collected through the Mosaic Standards Challenge. The Mosaic Standards Challenge asked participating laboratories analyze the same set of 7 samples using their own favored MGS laboratory methods. Each lab submitted their raw sequencing results and protocol information. The resulting MGS data was analyzed through a common bioinformatic pipeline and then evaluated to determine the effects of methodological choices.

This repository contains raw and intermediate data files as well as analysis code from the manuscript ?Evaluating the Analytical Performance of Direct-to-Consumer Gut Microbiome Testing Services?. In this analysis a pilot version of the homogenized whole human stool reference material was submitted as a sample to commercial direct to consumer microbiome testing companies. In addition, NIST conducted in house characterization by 16S amplicon sequencing and whole metagenomic sequencing (WMS) on the same sample. Raw sequencing data from the sequencing providers was not obtained for this study; however sequencing files (fastq) both 16S amplicon sequencing analysis and whole metagenomic sequencing (WMS) conducted at NIST are included. In addition, the fastq files from other donors that contributed to the pilot material and included in this analysis to represent biological diversity are also included in this record.

The repository contains the analysis and results collected during a metabolomics interlaboratory study. The study involved the experimental analysis of human stool from vegan and omnivore donors preserved in lyophilized format and aqueous phase, all stored at -80 C. The interlaboratory study (ILS) involved 18 participant institutions, and they were given the flexibility to use their preferred sample preparation method and analytical platform to analyze the stool samples. The analytical platforms used in the study were liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) to analyze the stool samples.Each participant submitted two lists of metabolites - one containing the Top 20 most abundant metabolites, and the other containing all annotated metabolites. The collected data was then analyzed to assess the suitability of a suite of candidate fecal reference material, ultimately aiming to enhance confidence in the measurements of gut metabolomics.

The raw sequencing data for this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB40814 with the following BioSample numbers: SAMEA7465213 (sample DWDS A1), SAMEA7465214 (DWDS A2), SAMEA7465217 (DWDS B1), SAMEA7465218 (DWDS B2), SAMEA7465220 (DWDS C1), SAMEA7465221 (DWDS C2), SAMEA7465222 (DWDS D1), SAMEA7465223 (DWDS D2), SAMEA7465226 (DWDS E1), and SAMEA7465227 (DWDS E2). This dataset is associated with the following publication: Gomez-Alvarez, V., S. Siponen, A. Kauppinen, A. Hokajarvi , A. Tiwari, A. Sarekoski, I.T. Miettinen, E. Torvinen, and T. Pitkanen. A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland. WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 229: 119495, (2023).

The raw sequencing data for this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB40814 with the following BioSample numbers: SAMEA7465213 (sample DWDS A1), SAMEA7465214 (DWDS A2), SAMEA7465217 (DWDS B1), SAMEA7465218 (DWDS B2), SAMEA7465220 (DWDS C1), SAMEA7465221 (DWDS C2), SAMEA7465222 (DWDS D1), SAMEA7465223 (DWDS D2), SAMEA7465226 (DWDS E1), and SAMEA7465227 (DWDS E2). This dataset is associated with the following publication: Gomez-Alvarez, V., S. Siponen, A. Kauppinen, A. Hokajarvi , A. Tiwari, A. Sarekoski, I.T. Miettinen, E. Torvinen, and T. Pitkanen. A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland. WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 229: 119495, (2023).

The raw sequencing data for this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB40814 with the following BioSample numbers: SAMEA7465213 (sample DWDS A1), SAMEA7465214 (DWDS A2), SAMEA7465217 (DWDS B1), SAMEA7465218 (DWDS B2), SAMEA7465220 (DWDS C1), SAMEA7465221 (DWDS C2), SAMEA7465222 (DWDS D1), SAMEA7465223 (DWDS D2), SAMEA7465226 (DWDS E1), and SAMEA7465226 (DWDS E2). This dataset is associated with the following publication: Tiwari, A., V. Gomez-Alvarez, S. Siponen, A. Sarekoski, A. Hokajärvi, A. Kauppinen, E. Torvinen, I.T. Miettinen, and T. Pitkänen. Bacterial Genes Encoding Resistance against Antibiotics and Metals in Well-Maintained Drinking Water Distribution Systems in Finland. Frontiers in Microbiology. Frontiers, Lausanne, SWITZERLAND, 12: 803094, (2022).

Draft genomes of various bacterial phyla isolated from different locations on the International Space Station, as part of the Microbial Tracking 2 mission (ISS-MOP).

A table (DP_SRA.xlsx) contains rows as sample and columns as entries representing the biosample accession number (NCBI), collection (date), library strategy, target (source), and sequencing (technology) for each individual sample. The zip file (Genome_Set01.zip) contain nine (9) fasta file (DP_bin_02.fasta, DP_bin_04.fasta, DP_bin_09.fasta, DP_bin_10.fasta, DP_bin_14.fasta, DP_bin_15.fasta, DP_bin_16a.fasta, DP_bin_20.fasta, DP_bin_23.fasta) with the contig sequences (i.e. binning) for each metagenome-assembled genomes (MAGs). These data are available from the NCBI Sequence Read Archive (SRA) under the BioProject (https://www.ncbi.nlm.nih.gov/bioproject) with accession number PRJNA646252 and the following BioSample numbers: SAMN15536103 to SAMN15536108. This dataset is associated with the following publication: Gomez-Alvarez, V., H. Liu, J. Pressman, and D. Wahman. Metagenomic Profile of Microbial Communities in a Drinking Water Storage Tank Sediment after Sequential Exposure to Monochloramine, Free Chlorine, and Monochloramine. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 1(5): 1283-1294, (2021).