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Mothur vs QIIME2 Analysis Outcomes

The document compares the Mothur and QIIME2 microbiome analysis workflows. Mothur takes fastq files as input and produces shared files containing OTUs, taxonomy files, and unweighted UniFrac scores as output. Unlike QIIME2, Mothur does not generate visualization data. The taxonomy classifications from Mothur and QIIME2 were different. Mothur is best for paired-end reads while QIIME2 can handle both single- and paired-end reads but requires more computing resources.

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Hari Sankar S
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10 views6 pages

Mothur vs QIIME2 Analysis Outcomes

The document compares the Mothur and QIIME2 microbiome analysis workflows. Mothur takes fastq files as input and produces shared files containing OTUs, taxonomy files, and unweighted UniFrac scores as output. Unlike QIIME2, Mothur does not generate visualization data. The taxonomy classifications from Mothur and QIIME2 were different. Mothur is best for paired-end reads while QIIME2 can handle both single- and paired-end reads but requires more computing resources.

Uploaded by

Hari Sankar S
Copyright
© All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd

Mothur workflow

Input:
-521 single reads fastq files
-metadata

Output:
-Shared file (OTUs)
-taxonomy file
-Unifrac scores
Mothur produced...
a unifrac unweighted score, show the significance of the distance between the two
groups, monozygous and the dizygous.

Unlike QIME2, no visualization data was produced.


Goodrich et. al. 2014
The taxonomy classification for in mothur yielded
different results.

Goodrich et. al. 2014


Limitations
Overall QIIME2 mothur
● 521 of 1081 samples ● QIIME2 possessed ● Not equipped for single-
analyzed updates that made end reads
○ Single-end reads specific steps different ● Does not output data for
● No categorization of from QIIME plotting unweighted
unrelated individuals ○ Denoising with UniFrac scores
(UN) available in DADA2
metadata

● Request all 1081 samples and ● Use for single- or paired-end ● Use for paired-end reads only
analyze these reads ● Use alternative tool for
● Request information on ● Must have computing producing visualizations
unrelated individuals and resources available ● Must have computing
account for this group resources available
Conclusions
● QIIME2 and mothur produced considerably different results
○ QIIME2 was more similar to the results reported in the paper
● The ideal tool depends on the dataset available
● The training data dictates the ability to make accurate and specific
classifications
● All methods are computationally demanding
● A better study could incorporate:
○ Paired-read data
○ Consistent computational resources
○ Metadata for unrelated (UN) individuals
References
1. Gilbert, J. A. et al. Current understanding of the human microbiome. Nature Medicine 24, 392–400 (2018).
2. Goodrich, J. K. et al. Human Genetics Shape the Gut Microbiome. Cell 159, 789–799 (2014).
3. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7,
335–336 (2010).
4. Schloss, P. mothur. (2017). Available at: [Link] (Accessed: November 30, 2018).

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