Minnesota Microbiome Data Engine Wiki¶

High-diversity samples¶

Low-diversity samples¶

Sample Collection¶

DNA extraction¶

Library Types¶

These preparation methods are currently supported by the UMGC

Earth Microbiome Protocol (EMP)

• V4
• V4 (version 2)
• ITS1

Dual-indexed

• V1-V3
• V4
• V4 + PNA blockers
• V3-V5
• V4-V6
• V5-V6
• V3 (in development)
• V3-V4 (in development)

IIS (in development)

• V4
• V4-V6

Process¶

The following steps are recommended for performing OTU picking using Qiime. Two packages are available to automate the process of running these steps on a dataset. If you have an MSI account you can use the “metagenomicsQC” package to automatically process a dataset using MSI computing resources and generate a html report summarizing the Qiime results. If you do not have access to MSI we provide a toolkit for generating a bash script to run all of these steps.

1. Configuring Qiime: FIX
2. Create Mapping File: FIX
3. Trimming/Filtering/Converting
   1. Overlapping paired-end reads: Read pairs are stitched together and amplicon primers are removed using PandaSeq. Sequence IDs are converted to Qiime format and fastq files are converted to fasta format.
   2. Non-overlapping paired-end reads: Samples with paired end reads that don’t overlap are treated like single-end reads; the second (R2) read is ignored
   3. Single-end reads: 3’ ends are quality trimmed and the amplicon primer is removed. Sequence IDs are converted to Qiime format and fastq files are converted to fasta format. (Qiime scripts convert_fasta_qual_fastq.py and split_libraries.py used)
4. Chimera Detection: Chimeras are detected using ChimeraSlayer’s usearch61 method.
5. OTU Picking: Qiime’s pick_open_reference_otus.py script is used to pick OTUs using usearch61.
6. Qiime Plots: A series of plots based on the OTU table are generated using Qiime
7. Alpha Diversity:
8. Normalization:
9. Beta Diversity:

Running at MSI¶

Running on a Mac or Linux computer¶

Qiime is a large software package with many dependencies that can be difficult to install. We recommend using MacQIIME is a precompiled installation of QIIME, with most of its dependecies, placed in one easy-to-install package. The MMDE-toolkit

Installing PICRUSt¶

Running PICRUSt¶