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Files for assessing the behavior of ADCL minimization under bootstrapping
Files for assessing the behavior of ADCL minimization under bootstrapping -
data for The Gene School: Metagenomics workshop
Precomputed data including a metagenomic assembly of multiple samples, reads from multiple samples mapped to the coassembly, metagenome-assembled genomes (MAGs), and anvio... -
Characteristics of study subjects.
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,... -
Banzai script
Analytical script for bioinformatics (Banzai Pipeline, O'Donnell, available at: https://github.com/jimmyodonnell/banzai/) used in publication. -
MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens o...
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... -
MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens o...
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... -
Bacterial strains and plasmids.
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... -
Informations concerning the samples and positive and negative controls multip...
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... -
MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens o...
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... -
R analysis script
R script used for analyses resulting in the publication. Calls data from associated Rdata file. -
Output of Phylosift (placement and summary files)
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... -
R data file
Contains: 1) detailed information about the meta-CGPs included in our analyses performed within; 2) gene-by-compendium matrices of PFP values (can be interpreted as FDR)... -
MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens o...
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... -
MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens o...
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... -
Metabarcoding data
otu.fa: a FASTA format file containing the sequences of all of the OTUs generated by the study; map.csv: a table reporting the number of reads of each OTU in each sequenced... -
"neotrop", "bv" and "tara" datasets used in the evaluation part of the main p...
Reference trees/alignments, as well as query data, for the "neotrop", "bv" and "tara" data sets. Made available with permission from the respective authors (see contained readme... -
MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens o...
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...
