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Supplemental Information

Comparisons between EBI and Kelpie community profiles

Excel spreadsheet containing EBI-generated profile for ERP008951, Kelpie profiles generated from the EBI-filtered '16S' reads, and comparisons at Class and Order levels.

DOI: 10.7287/peerj.preprints.27376v1/supp-1

Full CSM OTU table produced from both amplicon and Kelpie-generated sequences

Full OTU table produced from both amplicon and Kelpie-generated sequences for all three coal seam microbiome samples, ordered by total abundance. Red amplicon counts indicated that mapping the WGS reads for the sample back to the consensus sequence for the OTU showed that it had less than 90% kMer coverage. The green amplicon counts show where the WGS reads for a sample gave 100% coverage of the OTU sequence. This table is derived from the ‘AE’ tabs in the Excel spreadsheet ‘Kelpie - CSM.xlsx’ which is available as Supplemental Table S6.

DOI: 10.7287/peerj.preprints.27376v1/supp-2

Full CSM OTU table produced from amplicon,Kelpie sequences and primer-bound sequences extracted from full metaSPAdes assemblies and assemblies of the filtered 16S region reads

Full OTU table produced from amplicon, Kelpie-generated sequences and primer-bounded sequences extracted from full metaSPAdes assemblies for each WGS sample file, and from assemblies of the filtered 16S region reads, for all three coal seam microbiome samples, ordered by total abundance. Red amplicon counts indicated that mapping the WGS reads for the sample back to the consensus sequence for the OTU showed that it had less than 90% kMer coverage. The green amplicon counts show where the WGS reads for a sample gave 100% coverage of the OTU sequence. This table is derived from the ‘AESS’ tabs in the Excel spreadsheet ‘Kelpie - CSM.xlsx’ which is available as Supplemental Table S6.

DOI: 10.7287/peerj.preprints.27376v1/supp-3

Organisms in CAMI Low Complexity dataset, with presence in assembled contigs and Kelpie extended amplicons

The #strain column is the stated number of strains present in the WGS reads, and the Abundance column is the total abundance for the specified organism (including all its strains). These tables are derived from the Excel spreadsheet ‘Kelpie - CAMI Low.xlsx’ which is available as Supplemental Table S7. Part (a) includes all organisms, and Part (b) excludes those organisms that were found not to have a 16S V4 region in their assembled contigs.

DOI: 10.7287/peerj.preprints.27376v1/supp-4

Organisms in CAMI Medium Complexity dataset, with presence in assembled contigs and Kelpie extended amplicons

The #strain column is the stated number of strains present in the WGS reads, and the Abundance column is the total abundance for the specified organism (including all its strains). These tables are derived from the Excel spreadsheet ‘Kelpie - CAMI Medium.xlsx’ which is available as Supplemental Table S8. Part (a) includes all organisms, and Part (b) excludes those organisms that were found not to have a 16S V4 region in their assembled contigs.

DOI: 10.7287/peerj.preprints.27376v1/supp-5

Kelpie - CSM

Source spreadsheet for the CSM-derived tables and figures.

DOI: 10.7287/peerj.preprints.27376v1/supp-6

Kelpie - CAMI Low

Source spreadsheet for the CAMI Low-derived tables and figures.

DOI: 10.7287/peerj.preprints.27376v1/supp-7

Kelpie - CAMI Medium

Source spreadsheet for the CAMI Medium-derived tables and figures.

DOI: 10.7287/peerj.preprints.27376v1/supp-8

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Paul Greenfield conceived and designed the experiments, 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.

Nai Tran-Dinh conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

David Midgley conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

CSIRO Data Access Portal

DOI: 10.4225/08/59f98560eba25

DOI: 10.4225/08/5b31ca6373d48

GitHub

https://github.com/PaulGreenfieldOz/WorkingDogs

Funding

The authors received no funding for this work.


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