TODO: OTU clustering
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.
- Configuring Qiime: FIX
- Create Mapping File: FIX
- 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.
- 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
- 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)
- Chimera Detection: Chimeras are detected using ChimeraSlayer’s usearch61 method.
- OTU Picking: Qiime’s pick_open_reference_otus.py script is used to pick OTUs using usearch61.
- Qiime Plots: A series of plots based on the OTU table are generated using Qiime
- Alpha Diversity:
- Beta Diversity:
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
Generate QIIME bash script:
qiime-1.9.1.pl > qiime.sh
Execute QIIME bash script: