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Microbiome helper is a series of scripts that help process and automate various microbiome and metagenomic bioinformatic tools. The main workflows are for analyzing 16S and metagenomic data. These tools are contained in an Ubuntu virtual box image for those who don't want to set up their own work environment.

These scripts were produced as part of the Integrated Microbiome Resource. It is important that you cite the tools that are wrapped by our scripts.

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Before getting started:

• These workflows start with raw paired-end MiSeq data in demultiplexed fastq format.

• Most of the commands allow parallel threads to be used with the -p option. Adjust according to your computer hardware abilities.

• These workflows can be completed in roughly 24 hours on a single quad-core desktop when starting with 25 million paired end reads.