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Microbiome Helper is a repository that contains several resources to help researchers working with microbial sequencing data:

• a series of scripts that help process and automate various microbiome and metagenomic bioinformatic tools.
• workflows for analyzing 16S/18S rRNA and metagenomic data using these tools.
• tutorials for researchers new to rRNA and/or metagenomic analyses.
• a Virtual Box image that can be used to run our workflows with little or not configuration.

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

Use the sidebar menu to navigate the wiki.

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.