q2-mOTUs beta release ๐ŸŽ‰

We are proud to announce beta release of the q2-mOTUs plugin :tada: :tada: :tada:

mOTU is a tool for taxonomical profiling of metagenomic data extensively validated during CAMI Challenge.

Principal concept

mOTU is an attempt to build a taxonomy utilizing genomic information about organisms formalized with the help of differences in 40 universal gene markers (40 MGs) sequences. The basic unit of the taxonomy is an mOTU, and thus it is used in the output. Detailed description of the approach can be found in the paper.

Installation

The installation steps are described in our GitHub repo: GitHub - motu-tool/q2-mOTUs

Tutorial

There are two ways to use mOTU-tool within QIIME 2

1. Direct profiling of metagenomic samples

qiime motus profile \
--i-samples artifacts/study-seqs.qza \
--p-threads 8 \
--o-table artifacts/motu-table.qza \
--o-taxonomy artifacts/motu-taxonomy.qza

2. Import of precomputed mOTUs tables

Attention: precomupted mOTU table should be generated from full taxonomy (-q flag) and counts (-c flag) profiles.

qiime motus import-table \
--i-motus-table $TMPDIR/merged.motus \
--o-table artifacts/motu-table.qza \
--o-taxonomy artifacts/motu-taxonomy.qza

Compatibility with other QIIME 2 tools

Core QIIME 2

We can make a summary of the FeatureTable[Frequency] artifact motu-table.qza.

qiime feature-table summarize \
--i-table artifacts/motu-table.qza \
--o-visualization visualizations/motu-table-summary.qzv

motu-table-summary.qzv

Other plugins

We can produce a beautiful Krona plot using q2-krona:

qiime krona collapse-and-plot \
--i-table artifacts/motu-table-feces.qza \
--i-taxonomy artifacts/motu-taxonomy.qza \
--o-krona-plot visualizations/motu-krona-feces.qzv

motu-krona-feces.qzv

Extended tutorial

Extended version of this tutorial can be found in GitHub repo: q2-mOTUs/tutorial at main ยท motu-tool/q2-mOTUs ยท GitHub

Issue reporting

We encourage users to report possible problems either through QIIME2 Forum or GitHub issue section. Me and @hjruscheweyh will provide the support.

Citation

If you use the tool, please cite:

Ruscheweyh, H.-J., Milanese, A., Paoli, L., Karcher, N., Clayssen, Q., Keller, M. I., โ€ฆ Sunagawa, S. (2022). Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome, 10 (1). doi:10.1186/s40168-022-01410-z

Yours sincerely
Valentyn Bezshapkin
on behalf of Sunagawa Lab

7 Likes

Very exciting, thanks for all of your hard work @crusher083! :partying_face:

It's on my to-do list to look over this plugin and play around with it - I'll hopefully get to this in the next couple of weeks! Really looking forward to it!

3 Likes