# Supplemental Material and dataset summaries to accompany MGPrimerEval paper
Citation: McNichol, J., Berube P.M., Biller, S.J., Fuhrman, J.A. "Evaluating and Improving SSU rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys" *mSystems* ([link to paper](https://journals.asm.org/doi/10.1128/mSystems.00565-21)).
Supplementary material is now included here as a PDF because mSystems does not allow more than 10 supplemental figures.
We have also added a copy of the SRA run table [here](https://osf.io/fxy4j/) for easy downloading and cross-referencing of metagenome and amplicon data.
Data output is organized into separate folders (zipped up here because I couldn't get the OSF cli working and you can't upload folder structures with the web interface):
* 2-unusual-environments.zip
Primer evaluation results from Guaymas Basin and Saanich inlet - unusual oceanic environments that cross redoxclines.
* 5-pelagic-datasets.zip
Primer evaluation results from BioGEOTRACES/HOT/BATS, Catalina/SPOT, Malaspina, MBARI bloom, Tara Oceans (<3 µm size fractions), representing "typical" oxic ocean environments. Summaries are provided for the latter 4 datasets and represent the coverage for individual taxa summed across all samples.
The file "BGT-Dimensions-Malaspina-MBARI-TARA.noMT.tsv" contains the data used to plot Fig 2.
* cyanobacteria-chloroplast-info.zip
Selected summaries for each primer set tested, showing which photosynthetic taxa are missed by particular primers.
* primer-improvements.zip
Scripts and examples about how one might improve a primer set. Contains information used to create 515Yp-min/926Rp-min primers discussed in the paper text.
* BioGEOTRACES_MG_SSU_rRNA_pyNAST_alignments.zip
Contains example SSU rRNA alignments for each of the 4 organismal groups across all the BioGEOTRACES/BATS/HOT samples, with 50 sequences subsampled from each sample. This data supports the claim in the text that "We observed relatively even recruitment of metagenomic reads across the SSU rRNA molecule (Supplementary Results), which indicates that each different primer region has broadly similar potential to generate accurate taxonomic profiles of naturally-occurring organisms.".
* BioGEOTRACES_taxonomy-comparisons-MG-vs-ASV.zip
This archive contains head-to-head taxonomic comparisons of relative abundances derived from phyloFlash-extracted MG SSU rRNA and the amplicon community profiles for the 272 samples discussed in the text. Please note that the rows do not line up; the first two columns are the metagenomic SSU rRNA relative abundance taxonomy data from phyloFlash, whereas the last three columns are the PCR amplicon sequence variant relative abundance taxonomic data from the same sample. This shows that the taxonomic composition derived from these two techniques is broadly similar within the resolution of the technique.
