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QIIME procedure for creating HMP mock community OTUs

QIIME OTUs were obtained using the procedure recommended by Bokulic et al. [1] for MiSeq and commands recommended by the QIIME developers for Titanium (J. Gregory Caporaso, personal communication).

The QIIME release version was 1.5.0 at the time this work was done (Oct. 2012). This version does not support SRA or FASTQ files that lack barcodes. Following the advice of the QIIME developers, FASTQ files were converted to FASTA using the convert_fastaqual_fastq.py script using the new -c fastq_to_fastaqual option from developer version 1.5.0-dev (git commit hash 4974f0fe84e6aa9e6f41aa65aacf6ad60bcb6576), downloaded from the QIIME github repository (http://github.com/qiime/qiime). OTUs were built from the FASTA reads using the v1.5.0 pick_otus.py script with default parameters.