The below datasets were generated for the manuscript:
Lindgreen, Adair & Gardner (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports. 6, 19233.
Results from individual metagenome tools are available on Github
For the benchmark, we created two sets of files (set A and set B) with three replicates in each (A1-A3 and B1-B3). Each of these contains paired end data (paired information indicated by _1 and _2, respectively). Due to size restrictions, each of the fastq files had to be split in two parts (-0 and -1) and should be concatenated before use.

These are available on Zenodo: