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Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics

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RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
59 days ago
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
RT @ScottTKelley: Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/…
Excited to announce the pre-print release of meta-SourceTracker, an expansion of SourceTracker to metagenomic datasets w/ diagnostics. Domain-specific source tracking results show mSourceTracker can derive novel biological insights into microbial migration https://t.co/LbAi84zB4D
Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics https://t.co/0ktveGO49o https://t.co/mprJDjXnSF
Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics https://t.co/xBmkhKj9JN Background. Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated w…
59 days ago
Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics https://t.co/xex0GAyJzF https://t.co/vQ4VIaB31A
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Supplemental Information

List of accession numbers

Accession numbers of metagenomes used to test mSourceTracker separated by environment type.

DOI: 10.7287/peerj.preprints.27869v1/supp-1

Python code

Modified python files for use in SourceTracker2.

DOI: 10.7287/peerj.preprints.27869v1/supp-2

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Jordan J McGhee performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Nick Rawson performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Barbara A Bailey contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Antonio Fernandez-Guerra conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Scott T Kelley conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

To implement mSourceTracker, replace the existing '_sourcetracker.py' and 'gibbs.py' files with the modified ones provided as supplemental files. To implement the diagnostic features, use the command --diagnostics in order to run the script and use the command --limit to set the value of the differences between the draws. The default limit was set at 5%. To change it to 10% the user would just enter --limit 0.10.

Here is a command line example:

sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example1/ --diagnostics --limit 0.10

Funding

This work was funded by a fellowship awarded to ST Kelley by the Alexander von Humboldt Foundation of German. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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