Files for assessing the behavior of ADCL minimization under bootstrapping

Contains more specific Genbank accession information relevant to the project.

Precomputed data including a metagenomic assembly of multiple samples, reads from multiple samples mapped to the coassembly, metagenome-assembled genomes (MAGs), and anvio...

Taxonomic binning of the gold standard pooled assembly Software: PhyloPythiaS+ SoftwareVersion: 1.4 DataURL: https://data.cami-challenge.org/participate SoftwareURL:...

Software: MetaPaletteSoftwareVersion: 1.0.0DataURL: https://data.cami-challenge.org/participateSoftwareURL: https://doi.org/10.5281/zenodo.1730624DockerImage:...

JA-1, first-generation Japanese-Americans; JA-2, second- or later-generation Japanese-Americans; BMI, body mass index; BP, blood pressure; 2-h, two-hour post-load; HOMA-IR,...

Analytical script for bioinformatics (Banzai Pipeline, O'Donnell, available at: https://github.com/jimmyodonnell/banzai/) used in publication.

Genome binning of the gold standard pooled assembly Software: CONCOCTSoftwareVersion: 1.0.0DataURL: https://data.cami-challenge.org/participateSoftwareURL:...

This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746...

This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746...

Genome binning of the gold standard pooled assembly Software: MetaBATSoftwareVersion: 2.12.1DataURL: https://data.cami-challenge.org/participateSoftwareURL:...

aProvided by Jon Beckwith.bIn the experiment with HU (Figure 2, Table 2) the LJ52 strain was used. It is referred to as MG1655 for simplicity.cObtained from The Coli Genetic...

This XLSX file contains the run names, the sample IDs, the sample types, the PCR IDs, the PCR replicate numbers, the localities, the rodent species and the fastq file names for...

This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run...

Software: CAMIARKQuikrSoftwareVersion: 1.0.0DataURL: https://data.cami-challenge.org/participateSoftwareURL: https://doi.org/10.5281/zenodo.1730572DockerImage:...

R script used for analyses resulting in the publication. Calls data from associated Rdata file.

Software: FOCUSSoftwareVersion: 0.31DataURL: https://data.cami-challenge.org/participateSoftwareURL: https://github.com/metageni/FOCUSDockerImage:...

Text S6. How to run Step 4 (bioinformatics) of the SPIKEPIPE pipeline. Here we describe how to the user may apply SPIKEPIPE pipeline to a subset of the data used in this paper,...

Phylosift (Darling et al., PeerJ, 2014) was run on sequencing read sets obtained using Illumina technology on metagenomic DNA extracted from salivary samples of 33 human...

Clustering heatmap tool for kraken-style reports. Takes kraken style reports in text file format from eithr Kraken or Centrifuge (use centrifuge-kreport.pl). Produces a...